GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__PV4:5208455
          Length = 498

 Score =  575 bits (1481), Expect = e-168
 Identities = 277/489 (56%), Positives = 366/489 (74%), Gaps = 4/489 (0%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           WQ+ A SL I+ + FINGEY AA  N+TF+ + P+    L ++A    +D +RA++ AR 
Sbjct: 10  WQEMADSLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANARE 69

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
           VFERGDWS   P KRK V+ + ADL+EA+ +ELALLETLD GKPIR+S   D+ GAARA+
Sbjct: 70  VFERGDWSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARAL 129

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW  EA+DK+Y E+A T+ +E+ MI REPVGV+AAIVPWNFPLL+ CWKLGPALA GNSV
Sbjct: 130 RWSGEAVDKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSV 189

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           +LKPSEKSPL+AIR+A LA EAG+P GVLNV+ G+GH  G+AL+ H D+D + FTGST+ 
Sbjct: 190 VLKPSEKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 249

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
            KQL+  AG+SNMKRVWLEAGGKS NIVF D P+L++AA A A+ I +NQG+VC AG+RL
Sbjct: 250 AKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRL 309

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+E  + +E + L++ + Q WQPGHPLDPATT G ++D    ++V  +IR G ++G  L 
Sbjct: 310 LVESGVKEELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLR 369

Query: 369 DGRNAGLAAA----IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G    LA      + PTIF +V    ++++EEIFGPVL V  F   E+A+++ ND+ YG
Sbjct: 370 QGGQQVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYG 429

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484
           L A VWT D+S+AH+ ++ L++G V++N+Y+ GDMT PFGGYKQSGNGRDKSLHA +K+T
Sbjct: 430 LAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYT 489

Query: 485 ELKTIWISL 493
           E+K  WI+L
Sbjct: 490 EIKATWIAL 498


Lambda     K      H
   0.317    0.133    0.389 

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: 664
Number of extensions: 18
Number of successful extensions: 2
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: 495
Length of database: 498
Length adjustment: 34
Effective length of query: 461
Effective length of database: 464
Effective search space:   213904
Effective search space used:   213904
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