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.4060758.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.28
//
[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:

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:

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:

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:

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