GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF2231
          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:

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