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_RS24025 RR42_RS24025 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__Cup4G11:RR42_RS24025
          Length = 507

 Score =  805 bits (2080), Expect = 0.0
 Identities = 394/493 (79%), Positives = 440/493 (89%), Gaps = 1/493 (0%)

Query: 13  KLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGA 72
           KLLIDG++VES + +W ++VNPATQQV+ +VPFAT  EVDAAI++A RAF TW+ TP+GA
Sbjct: 16  KLLIDGKFVESDSNQWGNVVNPATQQVIGRVPFATVEEVDAAIASAQRAFLTWRNTPLGA 75

Query: 73  RMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFA 132
           R+R+MLK Q L+R + +RIA  L+ EQGKT+ DA+GDIFRGLEVVEHACS+G+LQMGEFA
Sbjct: 76  RLRVMLKFQDLVRRNMERIARTLTAEQGKTLPDAQGDIFRGLEVVEHACSVGTLQMGEFA 135

Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192
           ENVAGGVDTYTLRQPIGVCAGITPFNFP MIPLWMFPMAI CGNTFVLKPSEQDP+STM 
Sbjct: 136 ENVAGGVDTYTLRQPIGVCAGITPFNFPGMIPLWMFPMAIVCGNTFVLKPSEQDPLSTME 195

Query: 193 LVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRV 252
           LVELA+EAG+PPGVLNVVHGGK VVD LCTH D+KA+SFVGST VGTHVY+L  KHGKRV
Sbjct: 196 LVELAMEAGVPPGVLNVVHGGKTVVDMLCTHPDVKAISFVGSTHVGTHVYNLGSKHGKRV 255

Query: 253 QSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKALA 312
           QSMMGAKNHAVVLPDANR+Q LNALVGAGFGAAGQRCMATSVVVLVG ++ WLP+L   A
Sbjct: 256 QSMMGAKNHAVVLPDANRQQTLNALVGAGFGAAGQRCMATSVVVLVGQSRDWLPELVEKA 315

Query: 313 QKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNFVG 372
           + LKVNAG EPGTDVGPV+SK A AR+  LIE G++ GA L LDGRD+ VPGYE GNFVG
Sbjct: 316 KLLKVNAGHEPGTDVGPVMSKAAHARVTGLIEEGVQAGAALLLDGRDVKVPGYESGNFVG 375

Query: 373 PTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKF 432
           PT+FSGV+P+M IYTQEIFGPV+VVLEVDTLD+AIALVN NP GNG GLFTQSGAAARKF
Sbjct: 376 PTIFSGVSPDMSIYTQEIFGPVVVVLEVDTLDEAIALVNRNPMGNGVGLFTQSGAAARKF 435

Query: 433 QTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDDD 492
           Q+EIDVGQVGINIPIPVPVP+FSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDD 
Sbjct: 436 QSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDDT 495

Query: 493 SVNDGVNTTIHLR 505
              +GVNTTI LR
Sbjct: 496 PA-EGVNTTIALR 507


Lambda     K      H
   0.319    0.135    0.397 

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: 844
Number of extensions: 27
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 507
Length adjustment: 34
Effective length of query: 471
Effective length of database: 473
Effective search space:   222783
Effective search space used:   222783
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_RS24025 RR42_RS24025 (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.30448.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-231  753.0   1.5     7e-231  752.9   1.5    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS24025  RR42_RS24025 methylmalonate-semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS24025  RR42_RS24025 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  752.9   1.5    7e-231    7e-231       2     477 .]      16     491 ..      15     491 .. 1.00

  Alignments for each domain:
  == domain 1  score: 752.9 bits;  conditional E-value: 7e-231
                                 TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                               k+lidGkfve+ s+++++v npat++v+++v++a++eevdaa+asa+++f++w++t++  r rv+l++q
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025  16 KLLIDGKFVESDSNQWGNVVNPATQQVIGRVPFATVEEVDAAIASAQRAFLTWRNTPLGARLRVMLKFQ 84 
                                               789****************************************************************** PP

                                 TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGv 139
                                                l++ + + ia+ ++aeqGktl da+Gd++rGlevvehacsv +l +Ge  e+va  vd+y++rqp+Gv
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025  85 DLVRRNMERIARTLTAEQGKTLPDAQGDIFRGLEVVEHACSVGTLQMGEFAENVAGGVDTYTLRQPIGV 153
                                               ********************************************************************* PP

                                 TIGR01722 140 vaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdr 208
                                               +aGitpfnfp miplwmfp+ai+cGntfvlkpse++p+++++l el  eaG+p GvlnvvhG+k  vd+
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025 154 CAGITPFNFPGMIPLWMFPMAIVCGNTFVLKPSEQDPLSTMELVELAMEAGVPPGVLNVVHGGKTVVDM 222
                                               ********************************************************************* PP

                                 TIGR01722 209 llehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqr 277
                                               l+ hpdvka+sfvGs++vg ++y+ gs+hgkrvq+++Gaknh+vvlpda+++++l+alvga +GaaGqr
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025 223 LCTHPDVKAISFVGSTHVGTHVYNLGSKHGKRVQSMMGAKNHAVVLPDANRQQTLNALVGAGFGAAGQR 291
                                               ********************************************************************* PP

                                 TIGR01722 278 cmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldG 346
                                               cma s++vlvG+ +++++e++e+a+ ++v+ag++pg+++Gp+++k+a++rv+ li++g++ Ga +lldG
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025 292 CMATSVVVLVGQSRDWLPELVEKAKLLKVNAGHEPGTDVGPVMSKAAHARVTGLIEEGVQAGAALLLDG 360
                                               ********************************************************************* PP

                                 TIGR01722 347 rgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdG 415
                                               r +kv Gye GnfvG+t++++v pdm+iy +eifGpv+vvle+dtl+eai+l+n +p GnG  +ft++G
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025 361 RDVKVPGYESGNFVGPTIFSGVSPDMSIYTQEIFGPVVVVLEVDTLDEAIALVNRNPMGNGVGLFTQSG 429
                                               ********************************************************************* PP

                                 TIGR01722 416 aaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               aaarkfq ei+vGqvG+n+pipvp+p+fsftG+++s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__Cup4G11:RR42_RS24025 430 AAARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 491
                                               ************************************************************** 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.86
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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