Alignments for a candidate for mmsA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Shewanella amazonensis SB2B

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__SB2B:6938547
          Length = 496

 Score =  634 bits (1634), Expect = 0.0
 Identities = 304/498 (61%), Positives = 385/498 (77%), Gaps = 2/498 (0%)

Query: 1   MTTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTP 60
           M +I H +NGQ    + R+Q VF PATGE   Q+ LAST+ V +AI+ A+ AF +W    
Sbjct: 1   MQSITHFVNGQHTAPSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMT 60

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

Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180
           EH+  VG G+D+W+  QP+GVVAGI PFNFPVMVP+WMFP+AI CGN F++KPSE+DPSS
Sbjct: 121 EHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSS 180

Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANG 240
            + IA+LL+EAGLPDGV NVVNGDKEAVD LL    ++AVSFVGSTPIAEYIY TASA+G
Sbjct: 181 VMRIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYATASAHG 240

Query: 241 KRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSK 300
           KR QALGGAKNH ++MPDAD+D AVN L+GAA+GS+GERCMA+SV +AVGD AGDALV K
Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGD-AGDALVEK 299

Query: 301 MTQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHEN 360
           +   +  LKVG       + GP+I+ QH +KV  Y+ +  ++GA+++VDGR+  + +  N
Sbjct: 300 LLPKIAALKVGNGLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVDGRELSMEDKAN 359

Query: 361 GFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGE 420
           G+F+G  L DHVTP+M+ Y+EEIFGPVL +VRV     A+ LI+ HE+GNGT IFT+ GE
Sbjct: 360 GYFLGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFGNGTAIFTQSGE 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 WPQ-GKQLAAEFVMPTMK 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: 727
Number of extensions: 24
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 6938547 Sama_2650 (methylmalonate-semialdehyde dehydrogenase (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.24905.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.6e-210  684.2   0.6   5.2e-210  684.0   0.6    1.0  1  lcl|FitnessBrowser__SB2B:6938547  Sama_2650 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938547  Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.0   0.6  5.2e-210  5.2e-210       2     477 .]       5     480 ..       4     480 .. 0.99

  Alignments for each domain:
  == domain 1  score: 684.0 bits;  conditional E-value: 5.2e-210
                         TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                        h+++G+   + s++   v +pat+e  a+v+ as++ev +a+a a+ +f +w++ + ++rar+l++++al++++ d
  lcl|FitnessBrowser__SB2B:6938547   5 THFVNGQHT-APSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMTPLNRARILFKFKALVEANMD 80 
                                       688888875.56788899*********************************************************** PP

                         TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplw 155
                                       e+a+li+ e+Gk+l+dakG+++rGlevve+ac+++ ll+Ge + +v + vd ++++qplGvvaGi+pfnfp m+p+w
  lcl|FitnessBrowser__SB2B:6938547  81 ELAQLITREHGKVLDDAKGELIRGLEVVEFACGIPHLLKGEHTAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMW 157
                                       ***************************************************************************** PP

                         TIGR01722 156 mfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiye 232
                                       mfp+aiacGntf++kpsek+ps+ +++aell+eaG+pdGv+nvv Gdkeavd+ll h d++avsfvGs++++eyiy 
  lcl|FitnessBrowser__SB2B:6938547 158 MFPIAIACGNTFIMKPSEKDPSSVMRIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYA 234
                                       ***************************************************************************** PP

                         TIGR01722 233 tgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvga 308
                                       t+sahgkrvqal+Gaknhm+++pdad+++a++al+gaa+G+aG+rcmais++++vG+a + lve++  +++ ++vg 
  lcl|FitnessBrowser__SB2B:6938547 235 TASAHGKRVQALGGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGDAgDALVEKLLPKIAALKVGN 311
                                       **********************************************************999**************** PP

                         TIGR01722 309 gddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlv 385
                                       g  p  e+Gpli+ q+ ++v+s++++g++eGa++l+dGr + +e   +G f+G +l+++v p+m+iykeeifGpvl 
  lcl|FitnessBrowser__SB2B:6938547 312 GLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVDGRELSMEDKANGYFLGACLFDHVTPQMSIYKEEIFGPVLS 388
                                       ***************************************************************************** PP

                         TIGR01722 386 vleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkq 462
                                       ++++  ++ a++lin+  +GnGtaift++G aar+f h+++vG+vGvnvpipvp++f+sf+Gwk slfG lh++G +
  lcl|FitnessBrowser__SB2B:6938547 389 IVRVPDYNSALQLINDHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPD 465
                                       ***************************************************************************** PP

                         TIGR01722 463 Gvrfytrlktvtarw 477
                                       Gvrfyt+ k++tarw
  lcl|FitnessBrowser__SB2B:6938547 466 GVRFYTKRKAITARW 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.08
//
[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