GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Shewanella loihica PV-4

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__PV4:5209190
          Length = 501

 Score =  748 bits (1932), Expect = 0.0
 Identities = 359/496 (72%), Positives = 415/496 (83%)

Query: 1   MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKE 60
           M+  V+H I G F+ G G Q+I V+NP +N  +A I  A+ E+VE A+ASA++ FA+WKE
Sbjct: 1   MTTQVKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKE 60

Query: 61  TPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLL 120
            PVSERARVM RYQ LLK HHDE+A I++ E GKTFEDAKGDVWRGIEV EHACN+ SL+
Sbjct: 61  VPVSERARVMFRYQHLLKLHHDEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLI 120

Query: 121 MGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVP 180
           MGETVENVAR+IDTYS TQPLGVC GITPFNFPAMIPLWMFPLAIACGN F+LKPSEQ P
Sbjct: 121 MGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDP 180

Query: 181 LTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTA 240
           LT  RL ELF EAGAPKGVLQ+VHG K  VD LL H  +KA+SFVGSV VGQY+Y TGT 
Sbjct: 181 LTPQRLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTD 240

Query: 241 HNKRVQSFAGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPE 300
           + KRVQ+FAGAKNH VIMPDA+K QVI+NLVGASVGAAGQRCMA+SVAV VG A++WIPE
Sbjct: 241 NLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPE 300

Query: 301 IRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPD 360
           +RDA+AKVRPG WDD  A+YGPVI+P AKAR+ +LI QG EEGA+ LLDG  + VEGY +
Sbjct: 301 LRDAIAKVRPGVWDDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYEN 360

Query: 361 GNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGA 420
           GNWVGPT+F  V  DM+IY+EE+FGPVLC  EV+SLE+AI L+N SPYGNGTSIFT+ GA
Sbjct: 361 GNWVGPTMFTNVTTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGA 420

Query: 421 AARTFQHHIEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTAR 480
           AAR +QH+IEVGQVGIN+PIPVPLPFFSFTGWKGSFYGD HAYGKQ VRFYTETKT+TAR
Sbjct: 421 AARKYQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTITAR 480

Query: 481 WFDSDSVAGTNFSIQM 496
           WF++D V   + +  M
Sbjct: 481 WFETDIVEAEHHAPNM 496


Lambda     K      H
   0.319    0.135    0.406 

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: 808
Number of extensions: 34
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: 497
Length of database: 501
Length adjustment: 34
Effective length of query: 463
Effective length of database: 467
Effective search space:   216221
Effective search space used:   216221
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 5209190 Shew_1668 (methylmalonate-semialdehyde dehydrogenase (RefSeq))
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.12021.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-254  830.9   1.8   1.7e-254  830.7   1.8    1.0  1  lcl|FitnessBrowser__PV4:5209190  Shew_1668 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209190  Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.7   1.8  1.7e-254  1.7e-254       1     477 []       5     481 ..       5     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 830.7 bits;  conditional E-value: 1.7e-254
                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                      vkh+idG+f+ g +++ i v+npa+nev+a +  a++eev++a+asa+++fa+w+e +v+erarv++ryq llk h+d
  lcl|FitnessBrowser__PV4:5209190   5 VKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKEVPVSERARVMFRYQHLLKLHHD 82 
                                      89**************************************************************************** PP

                        TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwm 156
                                      eia +++ e Gkt+edakGdv+rG+ev ehac+++sl++Getve+va+++d+ys++qplGv+aGitpfnfpamiplwm
  lcl|FitnessBrowser__PV4:5209190  83 EIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWM 160
                                      ****************************************************************************** PP

                        TIGR01722 157 fplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetg 234
                                      fplaiacGntfvlkpse++p++  +l el++eaGap+Gvl++vhGdk avd ll h d+ka+sfvGsv vg+yiy+tg
  lcl|FitnessBrowser__PV4:5209190 161 FPLAIACGNTFVLKPSEQDPLTPQRLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTG 238
                                      ****************************************************************************** PP

                        TIGR01722 235 sahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddp 312
                                      + + krvqa+aGaknh v++pda+k++++++lvga+vGaaGqrcma+s+av vG+ak++++e+r++++kvr+g +dd 
  lcl|FitnessBrowser__PV4:5209190 239 TDNLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPELRDAIAKVRPGVWDDK 316
                                      ****************************************************************************** PP

                        TIGR01722 313 gaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390
                                       a +Gp+i+++ak+rv +lia+g +eGae lldG  ++veGye+Gn+vG+t++++v +dm+iykeeifGpvl+ +e++
  lcl|FitnessBrowser__PV4:5209190 317 DAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNWVGPTMFTNVTTDMSIYKEEIFGPVLCCMEVE 394
                                      ****************************************************************************** PP

                        TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfyt 468
                                      +leeai+l+n+spyGnGt+ift+ Gaaark+qh+ievGqvG+nvpipvplpffsftGwk+s++Gd+h+yGkq vrfyt
  lcl|FitnessBrowser__PV4:5209190 395 SLEEAIELVNNSPYGNGTSIFTACGAAARKYQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYT 472
                                      ****************************************************************************** PP

                        TIGR01722 469 rlktvtarw 477
                                      ++kt+tarw
  lcl|FitnessBrowser__PV4:5209190 473 ETKTITARW 481
                                      ********* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.35
//
[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:

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:

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:

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:

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