Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate RR42_RS28560 RR42_RS28560 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_05990
         (507 letters)



>FitnessBrowser__Cup4G11:RR42_RS28560
          Length = 506

 Score =  814 bits (2103), Expect = 0.0
 Identities = 401/501 (80%), Positives = 448/501 (89%)

Query: 7   PETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQT 66
           P      VKLLI+G+WVES  TE+  +VNPATQQVLA+VP AT AEV+AA+ AAHRAF T
Sbjct: 6   PNAAAPTVKLLINGEWVESAATEFRPVVNPATQQVLAQVPLATAAEVNAAVGAAHRAFAT 65

Query: 67  WKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIG 126
           W+ TP+GAR+RIMLK QALIREHSKRIA +L+AEQGKT+ADAEGDIFRGLEVVEHACSIG
Sbjct: 66  WRHTPLGARLRIMLKYQALIREHSKRIAAILTAEQGKTLADAEGDIFRGLEVVEHACSIG 125

Query: 127 SLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSE 186
           +LQ G FAENVA  VDTYTL+QPIGVCAGITPFNFPAMIPLWMFPMAI CGNTFVLKPSE
Sbjct: 126 TLQQGGFAENVAATVDTYTLQQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSE 185

Query: 187 QDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDL 246
           QDP+STM LV+LAIEAG+PAGVLNVVHG ++VVDALCTH DIKAVSFVGSTAVGTHVY+L
Sbjct: 186 QDPLSTMELVKLAIEAGVPAGVLNVVHGAREVVDALCTHPDIKAVSFVGSTAVGTHVYNL 245

Query: 247 AGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQW 306
           AG HGKRVQSMMGAKNHAVVLPDA+RE  LNAL GA FGAAGQRCMATSV VLVGAA++W
Sbjct: 246 AGAHGKRVQSMMGAKNHAVVLPDAHREHTLNALAGAAFGAAGQRCMATSVAVLVGAAREW 305

Query: 307 LPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDITVPG 366
           LP+L   A  LKV AG+EPGTDV PV+S  A+ R+L LIE+G +EGA L LDGR++ V G
Sbjct: 306 LPELVKKAATLKVGAGNEPGTDVCPVVSVAARQRVLGLIEAGEREGATLALDGRNVQVAG 365

Query: 367 YEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQ 426
           Y +GNF+GPT+F+ VTT+M IYTQEIFGPVLVV+ V+TLD+AIALVN NPFGNGTG+FTQ
Sbjct: 366 YPEGNFIGPTVFADVTTEMSIYTQEIFGPVLVVIGVETLDEAIALVNRNPFGNGTGIFTQ 425

Query: 427 SGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTV 486
           SGAAARKFQ+EIDVGQVGINIPIPVPVP+FSFTGSRGSKLGDLGPYGKQVVQFYTQTKTV
Sbjct: 426 SGAAARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTV 485

Query: 487 TSRWFDDDSVNDGVNTTINLR 507
           T+RWFDD +VNDGVNTTI+LR
Sbjct: 486 TARWFDDATVNDGVNTTISLR 506


Lambda     K      H
   0.319    0.135    0.396 

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: 809
Number of extensions: 24
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: 507
Length of database: 506
Length adjustment: 34
Effective length of query: 473
Effective length of database: 472
Effective search space:   223256
Effective search space used:   223256
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 RR42_RS28560 RR42_RS28560 (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.24420.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-226  737.2   4.9   4.3e-226  737.0   4.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS28560  RR42_RS28560 methylmalonate-semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS28560  RR42_RS28560 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.0   4.9  4.3e-226  4.3e-226       1     477 []      13     489 ..      13     489 .. 1.00

  Alignments for each domain:
  == domain 1  score: 737.0 bits;  conditional E-value: 4.3e-226
                                 TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllry 69 
                                               vk+li+G+ ve++++++ pv npat++vla+v+ a+a+ev+aav +a+++fa+w++t++  r r++l+y
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560  13 VKLLINGEWVESAATEFRPVVNPATQQVLAQVPLATAAEVNAAVGAAHRAFATWRHTPLGARLRIMLKY 81 
                                               899****************************************************************** PP

                                 TIGR01722  70 qallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplG 138
                                               qal++eh + ia +++aeqGktl+da+Gd++rGlevvehacs+ +l +G   e+va  vd+y+++qp+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560  82 QALIREHSKRIAAILTAEQGKTLADAEGDIFRGLEVVEHACSIGTLQQGGFAENVAATVDTYTLQQPIG 150
                                               ********************************************************************* PP

                                 TIGR01722 139 vvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavd 207
                                               v+aGitpfnfpamiplwmfp+ai+cGntfvlkpse++p+++++l +l  eaG+p GvlnvvhG +e vd
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560 151 VCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPLSTMELVKLAIEAGVPAGVLNVVHGAREVVD 219
                                               ********************************************************************* PP

                                 TIGR01722 208 rllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGq 276
                                                l+ hpd+kavsfvGs+avg ++y+ + ahgkrvq+++Gaknh+vvlpda++e++l+al gaa+GaaGq
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560 220 ALCTHPDIKAVSFVGSTAVGTHVYNLAGAHGKRVQSMMGAKNHAVVLPDAHREHTLNALAGAAFGAAGQ 288
                                               ********************************************************************* PP

                                 TIGR01722 277 rcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlld 345
                                               rcma s+avlvGaa+e+++e++++a+ ++vgag++pg+++ p+++ +a++rv  li++g +eGa + ld
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560 289 RCMATSVAVLVGAAREWLPELVKKAATLKVGAGNEPGTDVCPVVSVAARQRVLGLIEAGEREGATLALD 357
                                               ********************************************************************* PP

                                 TIGR01722 346 GrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsd 414
                                               Gr+++v Gy+eGnf+G+t++++v ++m+iy +eifGpvlvv+ ++tl+eai+l+n +p+GnGt ift++
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560 358 GRNVQVAGYPEGNFIGPTVFADVTTEMSIYTQEIFGPVLVVIGVETLDEAIALVNRNPFGNGTGIFTQS 426
                                               ********************************************************************* PP

                                 TIGR01722 415 GaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               Gaaarkfq ei+vGqvG+n+pipvp+p+fsftG+++s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__Cup4G11:RR42_RS28560 427 GAAARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 489
                                               *************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (506 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.68
//
[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