Alignments for a candidate for mmsA in Haloterrigena daqingensis JX313

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Haloterrigena daqingensis JX313

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_076582800.1 BB347_RS14640 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q97YT9
         (492 letters)



>NCBI__GCF_001971705.1:WP_076582800.1
          Length = 493

 Score =  437 bits (1123), Expect = e-127
 Identities = 218/476 (45%), Positives = 313/476 (65%), Gaps = 2/476 (0%)

Query: 18  YINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRI 77
           Y++G +     D      NPA  E +  V FS++ +++EA+++  EAFE+W + P+  RI
Sbjct: 16  YVDGAWQTPTGDDEQALSNPATTEPLGSVTFSSESDIDEAVRAGNEAFEEWSQAPVEERI 75

Query: 78  QYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEHLD 137
           Q LF LK  LEE+ + +A ++VQ+HGKT+ EARG++RR IENVE A      +  G  L+
Sbjct: 76  QPLFRLKTLLEEHQDELAELLVQDHGKTLAEARGELRRGIENVEVACGIPSMMQSGSLLN 135

Query: 138 QVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPMDFI 197
             + E+DE+ VR+PLGVF  ITPFNFP M+P WFLPYA+  GN+ ++KPSE  P+    +
Sbjct: 136 -AAPEIDESAVRKPLGVFAAITPFNFPGMIPLWFLPYAVATGNSFILKPSEQNPLVATRL 194

Query: 198 IRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAGKNGKKAI 257
             + DE   P GVV +V+G  D V+  + ++ V+G++FVGST V K IYE A  NGK+  
Sbjct: 195 FELIDEAGFPDGVVQLVNGGVDTVNGLIDHEGVEGISFVGSTPVAKLIYERAAANGKRVQ 254

Query: 258 VQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKFIEAS 317
            Q GAKN ++V   ADL  A    VS+    AG+RCLA   ++    +Y+E     +E +
Sbjct: 255 AQGGAKNHIIVTETADLEFAAEKTVSSACACAGERCLANDIVLVEDGVYEEFTDLVVEET 314

Query: 318 KQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPNGYFLG 377
               +G GL+E  D+G +++++ ++R+  YI+ G+EEGA +LLDGRD ++  + +G FL 
Sbjct: 315 ASQVVGNGLNEETDIGALISEEHEQRVRDYIDTGVEEGATVLLDGRDAEIDGHEDGNFLA 374

Query: 378 PTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGYYARKF 437
           PTVF +V+ EM I++EEIFGPV  +  V ++D+AI  +NRS +GNA+S+FT SG  ARKF
Sbjct: 375 PTVFGDVSEEMTISQEEIFGPVLGLASVDSVDDAIERMNRSRFGNAASLFTGSGADARKF 434

Query: 438 RREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQ-IDSVDFFTDKKVVITRW 492
           R E   GN+G+N+G +APMAFF FGG K+SFFG LH Q  D + F+TDK V I RW
Sbjct: 435 RHEGEIGNLGVNVGTSAPMAFFHFGGWKDSFFGDLHAQGEDMIHFYTDKAVYIERW 490


Lambda     K      H
   0.319    0.139    0.398 

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: 617
Number of extensions: 19
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: 492
Length of database: 493
Length adjustment: 34
Effective length of query: 458
Effective length of database: 459
Effective search space:   210222
Effective search space used:   210222
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 WP_076582800.1 BB347_RS14640 (CoA-acylating methylmalonate-semialdehyde dehydrogenase)
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.3809121.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-162  527.5   0.0   1.7e-162  527.3   0.0    1.0  1  NCBI__GCF_001971705.1:WP_076582800.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001971705.1:WP_076582800.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.3   0.0  1.7e-162  1.7e-162       1     477 []      13     490 ..      13     490 .. 0.98

  Alignments for each domain:
  == domain 1  score: 527.3 bits;  conditional E-value: 1.7e-162
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           v+ ++dG+    ++d    +snpat e l+ v+++s  ++d+av + +e+f  w++++v er + l+r ++ll
  NCBI__GCF_001971705.1:WP_076582800.1  13 VENYVDGAWQTPTGDDEQALSNPATTEPLGSVTFSSESDIDEAVRAGNEAFEEWSQAPVEERIQPLFRLKTLL 85 
                                           67899******************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           +eh+de+a+l++ ++Gktl++a+G++ rG+e ve ac+++s+++     + a ++d +++r+plGv a itpf
  NCBI__GCF_001971705.1:WP_076582800.1  86 EEHQDELAELLVQDHGKTLAEARGELRRGIENVEVACGIPSMMQSGSLLNAAPEIDESAVRKPLGVFAAITPF 158
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfp miplw +p a+a Gn+f+lkpse++p+ a +l el+ eaG pdGv+++v G+ ++v+ l++h  v  +s
  NCBI__GCF_001971705.1:WP_076582800.1 159 NFPGMIPLWFLPYAVATGNSFILKPSEQNPLVATRLFELIDEAGFPDGVVQLVNGGVDTVNGLIDHEGVEGIS 231
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.k 291
                                           fvGs++v++ iye+++a+gkrvqa +Gaknh +v   ad+e a+++ v++a  +aG+rc+a  ++++   + +
  NCBI__GCF_001971705.1:WP_076582800.1 232 FVGSTPVAKLIYERAAANGKRVQAQGGAKNHIIVTETADLEFAAEKTVSSACACAGERCLANDIVLVEDGVyE 304
                                           *************************************************************998766544449 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                           e+ + ++e  +   vg g +  +++G li++++ +rv ++i++g++eGa vlldGr  +++G+e+Gnf+ +t+
  NCBI__GCF_001971705.1:WP_076582800.1 305 EFTDLVVEETASQVVGNGLNEETDIGALISEEHEQRVRDYIDTGVEEGATVLLDGRDAEIDGHEDGNFLAPTV 377
                                           99999***999999*********************************************************** PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           + +v  +m+i +eeifGpvl ++ +d++++ai+ +n s +Gn +++ft +Ga arkf+he e+G +Gvnv   
  NCBI__GCF_001971705.1:WP_076582800.1 378 FGDVSEEMTISQEEIFGPVLGLASVDSVDDAIERMNRSRFGNAASLFTGSGADARKFRHEGEIGNLGVNVGTS 450
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                            p++ff f+Gwkds+fGdlh+ G++ ++fyt+  +   rw
  NCBI__GCF_001971705.1:WP_076582800.1 451 APMAFFHFGGWKDSFFGDLHAQGEDMIHFYTDKAVYIERW 490
                                           ********************************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (493 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: 00:00:00.01
# Mc/sec: 14.04
//
[ok]

This GapMind analysis is from Sep 24 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