Alignments for a candidate for acs in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Beijerinckia indica ATCC 9039

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_012383070.1 BIND_RS00265 acetyl-coenzyme A synthetase

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



>NCBI__GCF_000019845.1:WP_012383070.1
          Length = 645

 Score =  897 bits (2318), Expect = 0.0
 Identities = 426/636 (66%), Positives = 506/636 (79%), Gaps = 1/636 (0%)

Query: 7   YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YPV          + A YK MY++S+  PD FW E+ KR+DWIKP+T VK TSFD  +VD
Sbjct: 6   YPVSAYWNERAYINAAKYKDMYKRSIEEPDLFWGEEGKRIDWIKPYTKVKNTSFDPANVD 65

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126
           I+WF DG  NV+YNC+DRHLA RGDQ AI++EGDDP++SR ITY+ELH+ VC+ AN L+ 
Sbjct: 66  IRWFEDGITNVAYNCIDRHLATRGDQTAILFEGDDPADSRAITYKELHDSVCRLANVLKA 125

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
             V +GD V++Y+PMIPEA  AMLAC RIGAIHSV+FGGFSP++LAGRI  C+SKV+ITA
Sbjct: 126 HGVGKGDTVSLYLPMIPEAAFAMLACARIGAIHSVIFGGFSPDSLAGRIEGCRSKVLITA 185

Query: 187 DEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGT 246
           DEG+R G+K+PLKAN D A+       +Q +IV  RT G + W + RD+ YE+ +  A  
Sbjct: 186 DEGLRGGRKVPLKANADLAIAKTG-DIVQTMIVVTRTGGAVDWVEGRDVRYEEAIAAASP 244

Query: 247 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTAD 306
            C   E+ AE  LFILYTSGSTG PKGV H T GYL+YA++TH+ VFDY  G+VYWCTAD
Sbjct: 245 ECPLTEVEAEHPLFILYTSGSTGAPKGVVHCTGGYLVYASMTHQYVFDYHDGDVYWCTAD 304

Query: 307 VGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMA 366
           VGWVTGHSYIVYGPLANGATTL+FEGVPNYP ++R  +VIDKHKV+I YTAPTAIRA+M 
Sbjct: 305 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWEVIDKHKVTIFYTAPTAIRALMG 364

Query: 367 SGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPL 426
           SG A V+    +SLRLLGSVGEPINPEAW+WY++ VG+ERCPIVDTWWQTETGG+LI+PL
Sbjct: 365 SGEAPVKKTSRASLRLLGSVGEPINPEAWEWYHRVVGEERCPIVDTWWQTETGGILITPL 424

Query: 427 PGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFVD 486
           PGAT  KPGSAT PFFGV P +VD  G ++EG  EGNLVI DSWPGQ RT++GDHDRFV 
Sbjct: 425 PGATPEKPGSATLPFFGVKPQVVDATGAVLEGVCEGNLVIADSWPGQMRTIFGDHDRFVQ 484

Query: 487 TYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 546
           +YF T+ G YFTGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ES++VAH  V+EAA
Sbjct: 485 SYFSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRLGTAEVESSLVAHELVSEAA 544

Query: 547 VVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 606
           VVG PHDIKGQGIY YVTL  G E S+ LR EL  WVRK+IGPIA+PDV+ +A GLPKTR
Sbjct: 545 VVGYPHDIKGQGIYAYVTLMNGIEPSDRLRTELVTWVRKDIGPIATPDVVHFATGLPKTR 604

Query: 607 SGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           SGKIMRRILRKIA  E+  LGD+STLADP +V  LI
Sbjct: 605 SGKIMRRILRKIAEKEFSALGDVSTLADPTIVDDLI 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: 1408
Number of extensions: 56
Number of successful extensions: 2
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_012383070.1 BIND_RS00265 (acetyl-coenzyme A 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.16399.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 1014.2   0.0          0 1014.0   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012383070.1  BIND_RS00265 acetyl-coenzyme A s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012383070.1  BIND_RS00265 acetyl-coenzyme A synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1014.0   0.0         0         0       3     628 ..      19     641 ..      17     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1014.0 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhve 68 
                                               ++ +yk++y+++ie+p+ fw++++k +++w+kp++kv+++s++p   +++Wfedg +nv+ync+drh++
  lcl|NCBI__GCF_000019845.1:WP_012383070.1  19 NAAKYKDMYKRSIEEPDLFWGEEGK-RIDWIKPYTKVKNTSFDPanvDIRWFEDGITNVAYNCIDRHLA 86 
                                               6789*********************.5***************9988899******************** PP

                                 TIGR02188  69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRi 137
                                               +r d++ai +egd++  dsr++tY+el+++vcrlanvlk++Gv kgd+v++Ylpmipea++amlacaRi
  lcl|NCBI__GCF_000019845.1:WP_012383070.1  87 TRGDQTAILFEGDDPA-DSRAITYKELHDSVCRLANVLKAHGVGKGDTVSLYLPMIPEAAFAMLACARI 154
                                               ***************9.5*************************************************** PP

                                 TIGR02188 138 GavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtge 206
                                               Ga+hsv+f+Gfs+++la Ri+ +++k++itadeglRgg++++lk+++d a++k+ + v++++vv rtg 
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 155 GAIHSVIFGGFSPDSLAGRIEGCRSKVLITADEGLRGGRKVPLKANADLAIAKTGDIVQTMIVVTRTGG 223
                                               ********************************************************************* PP

                                 TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275
                                                v  w+egrDv +ee+++  as ec+ +++++e+plfiLYtsGstG PkGv+h+tgGyl++a++t++yv
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 224 AVD-WVEGRDVRYEEAIAA-ASPECPLTEVEAEHPLFILYTSGSTGAPKGVVHCTGGYLVYASMTHQYV 290
                                               *66.**************5.************************************************* PP

                                 TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
                                               fd++d+d++wCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+ srfwevi+k+kvtifYtaPtai
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 291 FDYHDGDVYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWEVIDKHKVTIFYTAPTAI 359
                                               ********************************************************************* PP

                                 TIGR02188 345 RalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgva 413
                                               Ralm  ge+ vkk+++ slr+lgsvGepinpeaweWy++vvG+e+cpivdtwWqtetGgilitplpg a
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 360 RALMGSGEAPVKKTSRASLRLLGSVGEPINPEAWEWYHRVVGEERCPIVDTWWQTETGGILITPLPG-A 427
                                               *******************************************************************.6 PP

                                 TIGR02188 414 telkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyf 482
                                               t+ kpgsatlP+fG++++vvd +g  +e   e g Lvi ++wP+++rti+gd++rfv++Yf++++g yf
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 428 TPEKPGSATLPFFGVKPQVVDATGAVLEGVCE-GNLVIADSWPGQMRTIFGDHDRFVQSYFSTYPGKYF 495
                                               **************************997666.89********************************** PP

                                 TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                               tGDg+rrd+dGy+wi+GRvDdvinvsGhrlgtae+es+lv+he v+eaavvg+p++ikg+ i+a+v+l+
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 496 TGDGCRRDADGYYWITGRVDDVINVSGHRLGTAEVESSLVAHELVSEAAVVGYPHDIKGQGIYAYVTLM 564
                                               ********************************************************************* PP

                                 TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstled 619
                                               +g+e+++ +l++el ++vrk igpia+pd +++++ lPktRsGkimRR+lrkiae+e ++lgdvstl+d
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 565 NGIEPSD-RLRTELVTWVRKDIGPIATPDVVHFATGLPKTRSGKIMRRILRKIAEKEfSALGDVSTLAD 632
                                               *******.5************************************************************ PP

                                 TIGR02188 620 psvveelke 628
                                               p++v++l++
  lcl|NCBI__GCF_000019845.1:WP_012383070.1 633 PTIVDDLIR 641
                                               *****9975 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 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.50
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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