Alignments for a candidate for acs in Pseudomonas baetica a390

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas baetica a390

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_100847194.1 C0J26_RS06710 acetate--CoA ligase

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



>NCBI__GCF_003031005.1:WP_100847194.1
          Length = 645

 Score =  823 bits (2126), Expect = 0.0
 Identities = 398/640 (62%), Positives = 480/640 (75%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  Y+ +Y++S+ +P  FW EQA R LDW  P+ TV++  +D  
Sbjct: 5   STFPKADAVRRAAQLSQDDYQRLYRESIEHPSAFWAEQALRFLDWSTPWQTVQR--YDLK 62

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
             +  WFA G LNVSYNC+DRHL +RGDQ A++WEGDDP+ES  ITY++LH  VC+ AN 
Sbjct: 63  AGEAAWFAGGKLNVSYNCIDRHLEQRGDQTALLWEGDDPAESAQITYKKLHHHVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEAV AMLAC RIGAIHSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAVYAMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK +PLK NVD AL N    ++  V+V +RT GN+ W + RD+WY   ++ 
Sbjct: 183 ITADEGVRGGKFVPLKQNVDKALQN--CPAVSTVVVVERTQGNVDWVEGRDLWYHQAVRD 240

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

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R  +VIDKHKV+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLMFEGVPSYPNSSRFWQVIDKHKVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G   ++     SLRLLGSVGEPINPEAW+WY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGAEPLKETSRQSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  +KPG AT+P FGV P L+D  G  I+GA  G L I  SWP Q R++YGD  R
Sbjct: 421 SPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYGDPQR 480

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

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E ++ L+ EL   V KEIG  A PD+IQWAP LP
Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGTEPNDELKKELLAHVSKEIGSFAKPDLIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVQGLID 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: 1352
Number of extensions: 72
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 WP_100847194.1 C0J26_RS06710 (acetate--CoA ligase)
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.4129840.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 1035.1   0.0          0 1034.9   0.0    1.0  1  NCBI__GCF_003031005.1:WP_100847194.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003031005.1:WP_100847194.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1034.9   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1034.9 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                           ++++y++ly+e+ie+p++fwa++a + l+w +p+++v++ +l++ +++Wf++g+lnvsync+drh+e+r d++
  NCBI__GCF_003031005.1:WP_100847194.1  20 SQDDYQRLYRESIEHPSAFWAEQALRFLDWSTPWQTVQRYDLKAgEAAWFAGGKLNVSYNCIDRHLEQRGDQT 92 
                                           5789*************************************9999**************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a+ wegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipeav+amlacaRiGa+hsvvf+G
  NCBI__GCF_003031005.1:WP_100847194.1  93 ALLWEGDDPAE-SAQITYKKLHHHVCRLANVLKSRGVKKGDRVCIYMPMIPEAVYAMLACARIGAIHSVVFGG 164
                                           *********96.************************************************************* PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+++l++Ri da++++vitadeg+Rggk ++lk++vd+al++++ +v++v+vv+rt+ +v  w+egrD+w++
  NCBI__GCF_003031005.1:WP_100847194.1 165 FSPDSLRDRILDADCRTVITADEGVRGGKFVPLKQNVDKALQNCP-AVSTVVVVERTQGNVD-WVEGRDLWYH 235
                                           ********************************************9.7*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           ++v++ +s++c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWv
  NCBI__GCF_003031005.1:WP_100847194.1 236 QAVRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWCTADVGWV 307
                                           ****7.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivygPLanGattl+fegvp+yp++srfw+vi+k+kv+ifYtaPta+Ralm++g e +k+++++slr+l
  NCBI__GCF_003031005.1:WP_100847194.1 308 TGHSYIVYGPLANGATTLMFEGVPSYPNSSRFWQVIDKHKVNIFYTAPTALRALMREGAEPLKETSRQSLRLL 380
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaweWy++vvG+++cpivdtwWqtetGgi+++pl + a  +kpg+at+P+fG++++++de+gke
  NCBI__GCF_003031005.1:WP_100847194.1 381 GSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKE 452
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++   + gvL+ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+
  NCBI__GCF_003031005.1:WP_100847194.1 453 IKGAGS-GVLAIKSSWPAQIRSVYGDPQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRI 524
                                           *98777.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++e l+kel ++v+keig++akpd i+++
  NCBI__GCF_003031005.1:WP_100847194.1 525 GTAEVESALVLHDSIAEAAVVGYPHDVKGQGIYAFVTPMNGTEPNDE-LKKELLAHVSKEIGSFAKPDLIQWA 596
                                           **********************************************5.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++
  NCBI__GCF_003031005.1:WP_100847194.1 597 PALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVQGLID 640
                                           ***************************************99875 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 32.31
//
[ok]

This GapMind analysis is from Sep 24 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
the source code
instructions for running GapMind on your computer

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