Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Ac3H11_4340 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4340
          Length = 505

 Score =  730 bits (1884), Expect = 0.0
 Identities = 355/497 (71%), Positives = 411/497 (82%)

Query: 2   TTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPP 61
           TT+GHLI+G+ V +  R+Q VFNPATG+    + LAS  TVE AI++A+ AFP WRNTPP
Sbjct: 9   TTVGHLIDGKSVADAERTQPVFNPATGQSTTSVALASKATVEAAIASAEAAFPAWRNTPP 68

Query: 62  LKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGE 121
           LKRARVM + K LLE++AD+I  LI  EHGK+  DA GELQRGIENVEYA  APELLKGE
Sbjct: 69  LKRARVMSKLKVLLEENADKIAALITAEHGKVLADAHGELQRGIENVEYASYAPELLKGE 128

Query: 122 HSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSST 181
           HSRNVGP IDSWSEFQ +GV AGITPFNFP MVPLWM+PMA+ CGN FVLKPSERDPSST
Sbjct: 129 HSRNVGPSIDSWSEFQALGVTAGITPFNFPAMVPLWMWPMAVACGNTFVLKPSERDPSST 188

Query: 182 LYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGK 241
           L+IAQL  EAGLP GV+NVVNGDK AVD LL D RVKAVSFVGSTPIAEYIY     +GK
Sbjct: 189 LFIAQLALEAGLPPGVLNVVNGDKLAVDTLLQDPRVKAVSFVGSTPIAEYIYSEGCKHGK 248

Query: 242 RCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKM 301
           R QALGGAKNHA++MPDAD+ NAV+ L+GAA+GS GERCMA+ + VAVGDA GDA+++ +
Sbjct: 249 RVQALGGAKNHAVLMPDADVGNAVSALMGAAYGSCGERCMAIPLLVAVGDAVGDAVIAGL 308

Query: 302 TQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENG 361
              + K+KVGP TD+ ND GP++T+ H EKV  Y++S   +GAT+VVDGR  KV  HE G
Sbjct: 309 KTEIAKMKVGPGTDNSNDMGPLVTKPHFEKVKAYVDSGVTEGATLVVDGRGVKVAGHEEG 368

Query: 362 FFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEA 421
           +F+G  L D+V P M  YQEEIFGPVL VVRV T+Q+AM LI+ HEYGNGTCIFTRDGEA
Sbjct: 369 YFLGACLFDNVKPGMKIYQEEIFGPVLGVVRVKTLQEAMQLINDHEYGNGTCIFTRDGEA 428

Query: 422 ARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRW 481
           ARYF+D+IQVGMVG+N+PLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKT+TQRW
Sbjct: 429 ARYFTDHIQVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQRW 488

Query: 482 PSAGVREGAEFSMPTMK 498
           PSAGVREGA FS P+ +
Sbjct: 489 PSAGVREGAVFSFPSSR 505


Lambda     K      H
   0.319    0.135    0.405 

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: 842
Number of extensions: 28
Number of successful extensions: 1
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: 498
Length of database: 505
Length adjustment: 34
Effective length of query: 464
Effective length of database: 471
Effective search space:   218544
Effective search space used:   218544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_4340 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.17008.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.4e-205  667.8   0.4     5e-205  667.6   0.4    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340  Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.6   0.4    5e-205    5e-205       1     477 []      11     488 ..      11     488 .. 0.99

  Alignments for each domain:
  == domain 1  score: 667.6 bits;  conditional E-value: 5e-205
                                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaer 62 
                                                      v hlidGk v   +++  pv npat++ ++ va as++ v+aa+asa  +f+aw++t+ ++r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340  11 VGHLIDGKSVAD-AERTQPVFNPATGQSTTSVALASKATVEAAIASAEAAFPAWRNTPPLKR 71 
                                                      679*****9975.57789******************************************** PP

                                        TIGR01722  63 arvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesv 124
                                                      arv+ + + ll+e+ d+ia li+ae+Gk+l+da+G++ rG+e ve+a   + ll+Ge + +v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340  72 ARVMSKLKVLLEENADKIAALITAEHGKVLADAHGELQRGIENVEYASYAPELLKGEHSRNV 133
                                                      ************************************************************** PP

                                        TIGR01722 125 akdvdvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaell 186
                                                        ++d +s  q lGv+aGitpfnfpam+plwm+p+a+acGntfvlkpse++ps+++ +a+l 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 134 GPSIDSWSEFQALGVTAGITPFNFPAMVPLWMWPMAVACGNTFVLKPSERDPSSTLFIAQLA 195
                                                      ************************************************************** PP

                                        TIGR01722 187 seaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGak 248
                                                      +eaG+p Gvlnvv Gdk avd+ll+ p vkavsfvGs++++eyiy+ g++hgkrvqal+Gak
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 196 LEAGLPPGVLNVVNGDKLAVDTLLQDPRVKAVSFVGSTPIAEYIYSEGCKHGKRVQALGGAK 257
                                                      ************************************************************** PP

                                        TIGR01722 249 nhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvga 308
                                                      nh+v++pdad  +a++al+gaa+G+ G+rcmai   v+vG+a  + ++  ++  ++k++vg+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 258 NHAVLMPDADVGNAVSALMGAAYGSCGERCMAIPLLVAVGDAvgDAVIAGLKTEIAKMKVGP 319
                                                      ****************************************998999**************** PP

                                        TIGR01722 309 gddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkp 370
                                                      g+d++ ++Gpl+tk + e+v+ +++sg+ eGa +++dGrg+kv G+eeG f+G +l+++vkp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 320 GTDNSNDMGPLVTKPHFEKVKAYVDSGVTEGATLVVDGRGVKVAGHEEGYFLGACLFDNVKP 381
                                                      ************************************************************** PP

                                        TIGR01722 371 dmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGv 432
                                                       mkiy+eeifGpvl v+++ tl+ea++lin+  yGnGt+ift+dG aar f  +i+vG+vGv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 382 GMKIYQEEIFGPVLGVVRVKTLQEAMQLINDHEYGNGTCIFTRDGEAARYFTDHIQVGMVGV 443
                                                      ************************************************************** PP

                                        TIGR01722 433 nvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                      nvp+pvp++++sf+Gwk slfGdlh+yG + vrfyt+ kt+t rw
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4340 444 NVPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQRW 488
                                                      ********************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (505 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.62
//
[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
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