GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Pseudomonas stutzeri RCH2

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2231 Psest_2276 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::B6ECN9
         (505 letters)



>lcl|FitnessBrowser__psRCH2:GFF2231 Psest_2276 NAD-dependent
           aldehyde dehydrogenases
          Length = 506

 Score =  325 bits (834), Expect = 2e-93
 Identities = 192/481 (39%), Positives = 276/481 (57%), Gaps = 16/481 (3%)

Query: 14  FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73
           +I GE+  P+K       +P N E+I   P +  ED++ A+ AA +A   D WG T+   
Sbjct: 22  YIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKALDAAHAAA--DAWGKTSVQD 79

Query: 74  RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132
           RA  L  IA ++     +LA  ET DNGK   E  + D+      F Y+A    A +   
Sbjct: 80  RALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGSA 139

Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192
             E+  H  ++  H   EPLGVVG I PWN+PLLM  WK+APALAAG   +LKP+E   +
Sbjct: 140 -AEINEHTAAYHFH---EPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPL 195

Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252
           + +   E+  ++ LPPG L+I+ G G EAG  L +   + KIAFTGS P G  IM  AA+
Sbjct: 196 SIMVFIEVVGDL-LPPGVLNIVQGFGREAGQALATSTRIAKIAFTGSTPVGSHIMRCAAE 254

Query: 253 LVKPVTLELGGKSPIVVFDDIHNLDTA-VEWTLFG---CFWTNGQICSATSRLIIQETIA 308
            + P T+ELGGKSP + F+DI N + A +E    G    F+  G++C+  SR +IQE+I 
Sbjct: 255 NIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVCTCPSRALIQESIF 314

Query: 309 PQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGGDRPE 368
             F+  +++  K IK  +PL+ D  +G   S  Q++KIL ++  A+ EGA IL GG   +
Sbjct: 315 EPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQEGAQILTGGAAEK 374

Query: 369 ---HLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGLGAA 425
               L  GYY+QPT+I      M +++EE+FGPV+ V TFK E EA+ +ANDT+FGLGA 
Sbjct: 375 LEGSLSTGYYVQPTLIKG-HNKMRVFQEEIFGPVVGVATFKDEAEALAIANDTEFGLGAG 433

Query: 426 ILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLNIKQ 485
           + ++D+ R  R  +  ++G VW NC         +GG K+SG GRE  +  L++Y   K 
Sbjct: 434 VWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKN 493

Query: 486 V 486
           +
Sbjct: 494 L 494


Lambda     K      H
   0.318    0.136    0.421 

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: 594
Number of extensions: 26
Number of successful extensions: 8
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: 505
Length of database: 506
Length adjustment: 34
Effective length of query: 471
Effective length of database: 472
Effective search space:   222312
Effective search space used:   222312
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)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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