Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14365
          Length = 645

 Score =  822 bits (2123), Expect = 0.0
 Identities = 399/640 (62%), Positives = 482/640 (75%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  Y+ +Y+QS+  PD FW EQAKR LDW  P+ +V+ T+    
Sbjct: 5   STFPKADAVRQAAQLSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
               +WFA   LNVSYNC+DRHLA+RG+Q AIIWEGDDP+ES +ITY++LH  VC+ AN 
Sbjct: 65  AA--QWFAGAQLNVSYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLAC RIGA+HSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK +PLK NVD AL +    ++  V+V + T   + W + RD+WY   ++ 
Sbjct: 183 ITADEGVRGGKYVPLKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRD 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GEV+WC
Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWC 300

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R  +VIDKH+V+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G   ++ +  +SLRLLGSVGEPINPEAWDWY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  +KPG ATRP FGV P L+D  G  I GA  G L I  SWPGQ R++YGD  R
Sbjct: 421 SPLVSAQRIKPGCATRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQR 480

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
            +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  +A
Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E S+AL+ EL   V +EIG  A PD+IQWAP LP
Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VVA LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVAGLID 640


Lambda     K      H
   0.318    0.135    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1340
Number of extensions: 69
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate AO353_14365 AO353_14365 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.25403.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
          0 1025.2   0.0          0 1025.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365  AO353_14365 acetyl-CoA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365  AO353_14365 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1025.0   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1025.0 bits;  conditional E-value: 0
                                     TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrh 66 
                                                   ++++y++ly+++ie+p+ fwa++ak+ l+w +p+++v++++ ++  ++Wf++++lnvsync+drh
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365  20 SQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTgAAQWFAGAQLNVSYNCIDRH 84 
                                                   5789**************************************9999******************* PP

                                     TIGR02188  67 vekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131
                                                   +++r +++aiiwegd++ e s ++tY++l++ vcrlanvlk+ Gvkkgdrv+iY+pmipea++am
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365  85 LAQRGEQTAIIWEGDDPAE-SLHITYQKLHHCVCRLANVLKSRGVKKGDRVCIYMPMIPEAAYAM 148
                                                   *****************96.********************************************* PP

                                     TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesve 196
                                                   lacaRiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rggk ++lk++vd+al +++ +v+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 149 LACARIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKYVPLKQNVDKALLSCP-AVS 212
                                                   ************************************************************9.7** PP

                                     TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhtt 261
                                                   +v+vv++t+ ev+ w+egrD+w+++++++ +s++c+pe++d+edplfiLYtsGstGkPkGvlhtt
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 213 TVVVVEHTQIEVN-WVEGRDLWYHQALRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTT 275
                                                   ***********66.**************7.*********************************** PP

                                     TIGR02188 262 gGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfw 326
                                                   gGyll+aa+t+kyvfd++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 276 GGYLLQAAMTFKYVFDYRDGEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFW 340
                                                   ***************************************************************** PP

                                     TIGR02188 327 eviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcp 391
                                                   +vi+k++v+ifYtaPta+Ralm++g e +k  ++ slr+lgsvGepinpeaw+Wy++ vG+++cp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 341 QVIDKHQVNIFYTAPTALRALMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCP 405
                                                   ***************************************************************** PP

                                     TIGR02188 392 ivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwP 456
                                                   ivdtwWqtetGgi+++pl + a  +kpg+at+P+fG++++++de+gke++   + gvL+ik++wP
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 406 IVDTWWQTETGGIMLSPLVS-AQRIKPGCATRPMFGVQPVLLDEHGKEISGAGS-GVLAIKSSWP 468
                                                   ********************.6***************************98777.8********* PP

                                     TIGR02188 457 smlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesal 521
                                                   +++r++ygd++r+++tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esal
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 469 GQIRSVYGDPQRMIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESAL 533
                                                   ***************************************************************** PP

                                     TIGR02188 522 vsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                                   v h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++ +l+kel ++v++eig++akpd i++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 534 VLHDSIAEAAVVGYPHDLKGQGIYAFVTPMNGIEPSD-ALKKELLAHVSQEIGSFAKPDLIQWAP 597
                                                   *************************************.5************************** PP

                                     TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                   +lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 598 ALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVAGLID 640
                                                   **************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.27
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources