Alignments for a candidate for mmsA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Azospirillum brasilense Sp245

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AZOBR_RS22500 AZOBR_RS22500 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__azobra:AZOBR_RS22500
          Length = 499

 Score =  742 bits (1915), Expect = 0.0
 Identities = 357/497 (71%), Positives = 416/497 (83%), Gaps = 1/497 (0%)

Query: 1   MTLIKHLIGGELIADTG-RTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNT 59
           M L+ HLIGG   A    R+AD+ NP+TGE V +VPLA R T++ AI AA+AAFPAWR T
Sbjct: 1   MPLVPHLIGGAADAPAETRSADIVNPATGETVGRVPLAGRATVESAIAAAEAAFPAWRAT 60

Query: 60  PPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILK 119
           PPAKRA+V+FRF+QLLE N +R+   I+ EHGKT+EDA GEL RGIENVEYA    ++LK
Sbjct: 61  PPAKRARVMFRFRQLLEDNADRVCAAITREHGKTLEDARGELTRGIENVEYACGIADLLK 120

Query: 120 GEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPS 179
           GE+S+NVGP ID+WS+FQP+GVVAGITPFNFPAMVPLWM+P+A+ACGN FILKPSERDPS
Sbjct: 121 GEHSKNVGPGIDSWSEFQPLGVVAGITPFNFPAMVPLWMFPVAVACGNCFILKPSERDPS 180

Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKR 239
           ++LL+A+L  EAGLP GVLNVVHGDK AVD L+  P V+A+SFVGSTP+AEY+Y+ GT  
Sbjct: 181 ASLLVAQLAQEAGLPPGVLNVVHGDKEAVDTLLTDPRVQAVSFVGSTPVAEYVYATGTAH 240

Query: 240 GKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQ 299
           GKRVQALGGAKNHA++MPDADLDNAVSA+MGAAYGSCGERCMAISV V VGD  AD +V 
Sbjct: 241 GKRVQALGGAKNHAIVMPDADLDNAVSAIMGAAYGSCGERCMAISVVVAVGDATADRVVA 300

Query: 300 KLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHE 359
            L  Q++ LK+GAGT  G DMGPLVT A  +KV G++D GVA+GAELVVDGRG  V GHE
Sbjct: 301 MLAEQVRSLKVGAGTGAGCDMGPLVTRAHFEKVKGFVDQGVAEGAELVVDGRGLVVPGHE 360

Query: 360 NGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDG 419
            GFFLGG LFDRVTP+M IY+EEIFGPVLC+VRV +++E M LI+ HEYGNGTC+FTRDG
Sbjct: 361 GGFFLGGCLFDRVTPDMRIYREEIFGPVLCVVRVATMQEGMDLIDAHEYGNGTCLFTRDG 420

Query: 420 EAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQ 479
           EAAR F D I+VGMVG+NVPLPVPV+YHSFGGWKRSLFGDL AYGPDGVRFYT+RK ITQ
Sbjct: 421 EAARYFTDAIKVGMVGINVPLPVPVSYHSFGGWKRSLFGDLAAYGPDGVRFYTRRKTITQ 480

Query: 480 RWPQRKSHEAAQFAFPS 496
           RWP     E AQF+FPS
Sbjct: 481 RWPTGGVREGAQFSFPS 497


Lambda     K      H
   0.319    0.137    0.411 

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: 851
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: 499
Length adjustment: 34
Effective length of query: 464
Effective length of database: 465
Effective search space:   215760
Effective search space used:   215760
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 AZOBR_RS22500 AZOBR_RS22500 (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.31683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-210  684.5   0.4   4.3e-210  684.3   0.4    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS22500  AZOBR_RS22500 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS22500  AZOBR_RS22500 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.3   0.4  4.3e-210  4.3e-210       1     477 []       4     482 ..       4     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 684.3 bits;  conditional E-value: 4.3e-210
                                 TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllry 69 
                                               v hli+G+    + ++  ++ npat+e++++v+ a  + v++a+a+a  +f+aw+ t+ a+rarv++r+
  lcl|FitnessBrowser__azobra:AZOBR_RS22500   4 VPHLIGGAADAPAETRSADIVNPATGETVGRVPLAGRATVESAIAAAEAAFPAWRATPPAKRARVMFRF 72 
                                               5699***9999999999**************************************************** PP

                                 TIGR01722  70 qallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplG 138
                                               ++ll+++ d +   i+ e+Gktleda+G++ rG+e ve+ac+++ ll+Ge +++v   +d +s  qplG
  lcl|FitnessBrowser__azobra:AZOBR_RS22500  73 RQLLEDNADRVCAAITREHGKTLEDARGELTRGIENVEYACGIADLLKGEHSKNVGPGIDSWSEFQPLG 141
                                               ********************************************************************* PP

                                 TIGR01722 139 vvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavd 207
                                               vvaGitpfnfpam+plwmfp+a+acGn+f+lkpse++psa++ +a+l +eaG+p GvlnvvhGdkeavd
  lcl|FitnessBrowser__azobra:AZOBR_RS22500 142 VVAGITPFNFPAMVPLWMFPVAVACGNCFILKPSERDPSASLLVAQLAQEAGLPPGVLNVVHGDKEAVD 210
                                               ********************************************************************* PP

                                 TIGR01722 208 rllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGq 276
                                               +ll  p v+avsfvGs++v+ey+y tg+ahgkrvqal+Gaknh++v+pdad+++a++a++gaa+G+ G+
  lcl|FitnessBrowser__azobra:AZOBR_RS22500 211 TLLTDPRVQAVSFVGSTPVAEYVYATGTAHGKRVQALGGAKNHAIVMPDADLDNAVSAIMGAAYGSCGE 279
                                               ********************************************************************* PP

                                 TIGR01722 277 rcmaisaavlvGaa..kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevl 343
                                               rcmais++v+vG+a  +++v  + e+++ ++vgag+ +g+++Gpl+t+++ e+v+ ++++g++eGae++
  lcl|FitnessBrowser__azobra:AZOBR_RS22500 280 RCMAISVVVAVGDAtaDRVVAMLAEQVRSLKVGAGTGAGCDMGPLVTRAHFEKVKGFVDQGVAEGAELV 348
                                               ************987799*************************************************** PP

                                 TIGR01722 344 ldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaift 412
                                               +dGrg+ v G+e G f+G +l++rv pdm+iy+eeifGpvl+v+++ t++e++ li++  yGnGt++ft
  lcl|FitnessBrowser__azobra:AZOBR_RS22500 349 VDGRGLVVPGHEGGFFLGGCLFDRVTPDMRIYREEIFGPVLCVVRVATMQEGMDLIDAHEYGNGTCLFT 417
                                               ********************************************************************* PP

                                 TIGR01722 413 sdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               +dG aar f   i+vG+vG+nvp+pvp++++sf+Gwk slfGdl +yG +Gvrfytr kt+t rw
  lcl|FitnessBrowser__azobra:AZOBR_RS22500 418 RDGEAARYFTDAIKVGMVGINVPLPVPVSYHSFGGWKRSLFGDLAAYGPDGVRFYTRRKTITQRW 482
                                               ***************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (499 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.68
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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