Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Acidovorax sp. GW101-3H11

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Ac3H11_2357 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= reanno::psRCH2:GFF2388
         (503 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2357
          Length = 507

 Score =  845 bits (2183), Expect = 0.0
 Identities = 421/496 (84%), Positives = 451/496 (90%)

Query: 8   PTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTP 67
           PTVKLLI G+F+ES T  WRDVVNPATQEVLARVPFAT EEID AVAS Q+AFKTW+KT 
Sbjct: 12  PTVKLLIGGKFVESKTTQWRDVVNPATQEVLARVPFATPEEIDAAVASAQEAFKTWKKTA 71

Query: 68  IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127
           IGARARIFLKYQQLIRENM ELAAILTAEQGKTL DAEGDVFRGLEVVEHAA IGNLQLG
Sbjct: 72  IGARARIFLKYQQLIRENMAELAAILTAEQGKTLPDAEGDVFRGLEVVEHAASIGNLQLG 131

Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187
           ELANNVA GVDTYTL+QPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV
Sbjct: 132 ELANNVAGGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 191

Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAG 247
           TMRL ELALEAG+PPGVLNV+HGG   VNAICDH DIKA+SFVGSTKVGTHVYNRAS  G
Sbjct: 192 TMRLVELALEAGIPPGVLNVIHGGEAAVNAICDHKDIKAISFVGSTKVGTHVYNRASLNG 251

Query: 248 KRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPDLV 307
           KRVQCMMGAKNHAIV+PDA+KEQTLN LAGAAFGAAGQRCMALSVVVLVGEAQ WIP+LV
Sbjct: 252 KRVQCMMGAKNHAIVMPDANKEQTLNALAGAAFGAAGQRCMALSVVVLVGEAQKWIPELV 311

Query: 308 AKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGN 367
           AKA+TLKV+AGVE GTDVGP+VSCAA DRV  LIERG+ +GA LELDGRNP V+GYE GN
Sbjct: 312 AKAKTLKVSAGVEKGTDVGPVVSCAAKDRVQSLIERGIADGATLELDGRNPEVAGYEKGN 371

Query: 368 FVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAA 427
           FVGPT+FSGV   MS+Y +EIFGPVLC+ AAA +DEAI  IN NPNGNGTAIFT+SGAAA
Sbjct: 372 FVGPTVFSGVKPGMSIYDQEIFGPVLCLSAAADIDEAIAFINDNPNGNGTAIFTQSGAAA 431

Query: 428 RHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTITERWF 487
           R FQEEIDVGQVGINVPIPVPVP+FSF+GSRASKLGDLGPYGKQVV FYTQTKT+T RWF
Sbjct: 432 RKFQEEIDVGQVGINVPIPVPVPLFSFSGSRASKLGDLGPYGKQVVLFYTQTKTVTARWF 491

Query: 488 DENEVGGPVNTTINLK 503
           D++ +   VNTTI+LK
Sbjct: 492 DDSTISHGVNTTISLK 507


Lambda     K      H
   0.318    0.134    0.394 

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: 824
Number of extensions: 26
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: 503
Length of database: 507
Length adjustment: 34
Effective length of query: 469
Effective length of database: 473
Effective search space:   221837
Effective search space used:   221837
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_2357 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
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.28597.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.1e-225  734.8   3.4   2.4e-225  734.6   3.4    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357  Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.6   3.4  2.4e-225  2.4e-225       1     477 []      14     490 ..      14     490 .. 1.00

  Alignments for each domain:
  == domain 1  score: 734.6 bits;  conditional E-value: 2.4e-225
                                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaer 62 
                                                      vk+li+Gkfve+k++++ +v npat+evla+v++a+ ee+daavasa+e+f +w++t++  r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357  14 VKLLIGGKFVESKTTQWRDVVNPATQEVLARVPFATPEEIDAAVASAQEAFKTWKKTAIGAR 75 
                                                      899*********************************************************** PP

                                        TIGR01722  63 arvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesv 124
                                                      ar++l+yq+l++e+  e+a +++aeqGktl da+Gdv+rGlevveha s+  l lGe+ ++v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357  76 ARIFLKYQQLIRENMAELAAILTAEQGKTLPDAEGDVFRGLEVVEHAASIGNLQLGELANNV 137
                                                      ************************************************************** PP

                                        TIGR01722 125 akdvdvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaell 186
                                                      a  vd+y++ qplGv+aGitpfnfpamiplwmfp+aia Gntfvlkpse++p  +++l el 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 138 AGGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELA 199
                                                      ************************************************************** PP

                                        TIGR01722 187 seaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGak 248
                                                      +eaG+p Gvlnv+hG++ av+ +++h d+ka+sfvGs++vg ++y+++s +gkrvq+++Gak
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 200 LEAGIPPGVLNVIHGGEAAVNAICDHKDIKAISFVGSTKVGTHVYNRASLNGKRVQCMMGAK 261
                                                      ************************************************************** PP

                                        TIGR01722 249 nhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagd 310
                                                      nh++v+pda+ke++l+al gaa+GaaGqrcma+s++vlvG+a+++++e++ +a+ ++v+ag 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 262 NHAIVMPDANKEQTLNALAGAAFGAAGQRCMALSVVVLVGEAQKWIPELVAKAKTLKVSAGV 323
                                                      ************************************************************** PP

                                        TIGR01722 311 dpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdm 372
                                                      + g+++Gp+++ +ak+rv+sli+ g+++Ga + ldGr+ +v Gye+GnfvG+t++++vkp m
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 324 EKGTDVGPVVSCAAKDRVQSLIERGIADGATLELDGRNPEVAGYEKGNFVGPTVFSGVKPGM 385
                                                      ************************************************************** PP

                                        TIGR01722 373 kiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnv 434
                                                      +iy +eifGpvl++  a  ++eai++in++p GnGtaift++Gaaarkfq ei+vGqvG+nv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 386 SIYDQEIFGPVLCLSAAADIDEAIAFINDNPNGNGTAIFTQSGAAARKFQEEIDVGQVGINV 447
                                                      ************************************************************** PP

                                        TIGR01722 435 pipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                      pipvp+p+fsf+G+++s  Gdl  yGkq v fyt++ktvtarw
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2357 448 PIPVPVPLFSFSGSRASKLGDLGPYGKQVVLFYTQTKTVTARW 490
                                                      ******************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (507 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: 00:00:00.02
# Mc/sec: 11.07
//
[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