GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Moritella dasanensis ArB 0140

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_017220578.1 A923_RS0105090 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-15736
         (480 letters)



>NCBI__GCF_000276805.1:WP_017220578.1
          Length = 487

 Score =  291 bits (744), Expect = 4e-83
 Identities = 168/467 (35%), Positives = 247/467 (52%), Gaps = 7/467 (1%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           +I G W  A       +N     + LG   +   A+  +AI AA  A P W     +++ 
Sbjct: 15  YIGGEW-QAGVSTVANINPSDISQNLGNFAQASTAQVHQAISAAKHAQPTWEKTPLEQKQ 73

Query: 74  TKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDVIPG 133
             L+   + LI   D+LGRL++ E+GKP  E +GEI  A  F ++FA E  R  GD    
Sbjct: 74  AVLQGIGDELIARCDELGRLLSSEEGKPFLEGRGEIYRAGQFFQYFAAEVLRQIGDSAAS 133

Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALV 193
            +P   + V ++ +GV A I+PWNFP A    K  PALA G +++ KPA+ TP SA+AL 
Sbjct: 134 VRPGVTVEVTREAVGVVAIISPWNFPTATAAWKIAPALAFGNSVIWKPANLTPASAVALT 193

Query: 194 ELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVS 253
           E+ HR G+P G  ++V GS  ++G  L ++  V  +SFTGS + GR++ A  A +  +  
Sbjct: 194 EIIHRQGLPAGTFNLVLGSGSEVGNVLINSTEVNGVSFTGSVDTGRKIAAATAPNFVRCQ 253

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKAAV 313
           LE+G     IV DDAD++ AVE  I   +   GQ C  ++RL + D ++DA+ E L   +
Sbjct: 254 LEMGSKNALIVADDADINIAVEATIAGSFSGAGQKCTASSRLVVMDGIHDAYVEALIKRM 313

Query: 314 AKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKSM----EGNFFEPT 369
           ++LK+G+ LE+G   GP++D K +      I  A + G  L  GG+ +    EG +  PT
Sbjct: 314 SQLKVGHALEDGVFMGPVVDGKQLDANLAWIDTARQSGGELAFGGERLSMEHEGFYMSPT 373

Query: 370 ILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAE 429
           + +N   D +V +EE F P+A + R  D  E IA +NDT FGL S    + L       +
Sbjct: 374 LFINTKNDWSVNQEEVFAPMASVIRVADLEEAIATTNDTRFGLTSGIITQSLRTSTLFKQ 433

Query: 430 ALEYGMVGVNTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIK 474
             + G V VN      +   PFGG K S  G RE  +Y  E Y  +K
Sbjct: 434 QAQTGCVMVNLPTAGTDYHVPFGGRKESSFGPREQGQYAKEFYTVVK 480


Lambda     K      H
   0.317    0.135    0.390 

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: 506
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: 480
Length of database: 487
Length adjustment: 34
Effective length of query: 446
Effective length of database: 453
Effective search space:   202038
Effective search space used:   202038
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 24 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