Alignments for a candidate for mmsA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Shewanella sp. ANA-3

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__ANA3:7025959
          Length = 496

 Score =  630 bits (1626), Expect = 0.0
 Identities = 305/498 (61%), Positives = 382/498 (76%), Gaps = 2/498 (0%)

Query: 1   MTTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTP 60
           M T+ H +NG+    +TRSQ +F PATGE   Q+ LAS   V  AI+ A+ AF TW    
Sbjct: 1   MLTMTHYVNGEHTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVT 60

Query: 61  PLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG 120
           PL RARV+F+FK L+EQH DE+ +LI  EHGK+  DA GEL RG+E VE+ACG P LLKG
Sbjct: 61  PLNRARVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKG 120

Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180
           EH+  VG G+D+WS  Q +GVVAGI PFNFPVMVP+WMFP+AI CGN F++KPSE+DPS+
Sbjct: 121 EHTEQVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSA 180

Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANG 240
            + IA+LL +AGLP GV NVVNGDKEAVD LL  + ++AVSFVGSTPIAEYIY TAS +G
Sbjct: 181 VMRIAELLTQAGLPAGVFNVVNGDKEAVDTLLSHEDIQAVSFVGSTPIAEYIYSTASKHG 240

Query: 241 KRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSK 300
           KR QALGGAKNH ++MPDAD+D AV+ L+GAA+GS+GERCMA+SV +AVGD  GD LV K
Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGD-VGDKLVDK 299

Query: 301 MTQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHEN 360
           +   +Q+LKVG       + GP+I+RQH  KV  ++++  ++GAT+VVDGRQ  V +H+ 
Sbjct: 300 LLPQIQQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQ 359

Query: 361 GFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGE 420
           G+F+G  L D+VTPEM  Y+EEIFGPVL +VRV     A+ LI+ HE+GNGT IFT+ GE
Sbjct: 360 GYFLGACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGE 419

Query: 421 AARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQR 480
           AAR+F  ++QVGMVG+N+P+PVP+A+HSFGGWKRSLFG LH +GPD VRFYTKRK +T R
Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479

Query: 481 WPSAGVREGAEFSMPTMK 498
           WP  G +  AEF MPTMK
Sbjct: 480 WP-VGKQTQAEFVMPTMK 496


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: 735
Number of extensions: 27
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: 498
Length of database: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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 7025959 Shewana3_3107 (methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq))
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.1407.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-210  686.2   0.6   1.3e-210  686.1   0.6    1.0  1  lcl|FitnessBrowser__ANA3:7025959  Shewana3_3107 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025959  Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.1   0.6  1.3e-210  1.3e-210       3     477 .]       6     480 ..       4     480 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.1 bits;  conditional E-value: 1.3e-210
                         TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrde 79 
                                       h+++G+   ++s++  ++ +pat+e  ++v+ as +ev aa+a a+ +f +w++ + ++rarvl++++al+++h de
  lcl|FitnessBrowser__ANA3:7025959   6 HYVNGEHT-AASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRARVLFKFKALVEQHMDE 81 
                                       78888765.6788999************************************************************* PP

                         TIGR01722  80 iaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwm 156
                                       +a+li++e+Gk+l+da+G+++rGlevve+ac+++ ll+Ge +e+v   vd +s++q lGvvaGi+pfnfp m+p+wm
  lcl|FitnessBrowser__ANA3:7025959  82 LAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTEQVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWM 158
                                       ***************************************************************************** PP

                         TIGR01722 157 fplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyet 233
                                       fp+aiacGntf++kpsek+psa +++aell++aG+p Gv+nvv Gdkeavd+ll h d++avsfvGs++++eyiy+t
  lcl|FitnessBrowser__ANA3:7025959 159 FPIAIACGNTFIMKPSEKDPSAVMRIAELLTQAGLPAGVFNVVNGDKEAVDTLLSHEDIQAVSFVGSTPIAEYIYST 235
                                       ***************************************************************************** PP

                         TIGR01722 234 gsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgag 309
                                       +s+hgkrvqal+Gaknhm+++pdad+++a++al+gaa+G+aG+rcmais++++vG++ ++lv+++  ++++++vg g
  lcl|FitnessBrowser__ANA3:7025959 236 ASKHGKRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVgDKLVDKLLPQIQQLKVGNG 312
                                       *********************************************************9******************* PP

                         TIGR01722 310 ddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvv 386
                                         p  e+Gpli++q+ ++v++++++g+keGa +++dGr ++v  +++G f+G +l+++v p+m+iy+eeifGpvl +
  lcl|FitnessBrowser__ANA3:7025959 313 LTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLGACLFDNVTPEMRIYREEIFGPVLSI 389
                                       ***************************************************************************** PP

                         TIGR01722 387 leadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqG 463
                                       +++  +  a++lin+  +GnGtaift++G aar+f h+++vG+vGvnvpipvp++f+sf+Gwk slfG lh++G +G
  lcl|FitnessBrowser__ANA3:7025959 390 VRVKDYASALALINQHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDG 466
                                       ***************************************************************************** PP

                         TIGR01722 464 vrfytrlktvtarw 477
                                       vrfyt+ k++tarw
  lcl|FitnessBrowser__ANA3:7025959 467 VRFYTKRKAITARW 480
                                       ************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (496 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.57
//
[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