GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Sphingomonas koreensis DSMZ 15582

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= reanno::Smeli:SM_b20891
         (477 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  271 bits (692), Expect = 5e-77
 Identities = 180/484 (37%), Positives = 259/484 (53%), Gaps = 39/484 (8%)

Query: 5   QNLIAGEWVGGDGVAN---INPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGIL 61
           ++ I GEWV  +G      INP+ T+  V E    S  DA  A+AAAKAAF ++SR+ + 
Sbjct: 6   KHYIGGEWVESEGGTRHDVINPA-TEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVD 64

Query: 62  ERHAILKKTADEILARKDELGRLLSREEGKTLA--------EGIGE---TVRAGQIFEFF 110
           ER A+L+    E   R  +L   ++ E G  ++         GIG    T+ A + FEF 
Sbjct: 65  ERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKAFEFS 124

Query: 111 A--GETLRLAGEVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTI 168
              G++L                 +  EP GVV +ITPWN+P+     K+APAL  GNT+
Sbjct: 125 EQIGQSL-----------------VVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTM 167

Query: 169 VFKPAELVPGCSWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTAT 228
           V KP+E  PG +    +I+ +AG+P GV NLV G G +VG A+    DV  ++FTGST  
Sbjct: 168 VLKPSEEAPGSAAIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRA 227

Query: 229 GKRVAVASVEHNRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIV 288
           G +VA  + E  ++   E+GGK+P V+L  ADLS AV+  + S   ++GQ C A +R++V
Sbjct: 228 GIQVAKNAAETVKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLV 287

Query: 289 TEGIHDRFVAAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFG 348
            E             +K +   D  + G HIGPVV+++Q  +    I  G +EGAKL  G
Sbjct: 288 HESQAAEAAQIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETG 347

Query: 349 GEVISRD-TPGFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGL 407
           G         G++++P LF+   N+M I+REEIFGPV  +I  +D +EA+ +ANDT +GL
Sbjct: 348 GPGRPDGIETGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGL 407

Query: 408 SSGIATTSLKHATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFY 467
           S+ +   S +          AGMV +N      D  +PFGG K S  G RE GK+    +
Sbjct: 408 SA-VLFGSPEEVKRVAPRLRAGMVYIN--GGQPDPSLPFGGYKQSGNG-REHGKFGLAEF 463

Query: 468 TNVK 471
             VK
Sbjct: 464 MEVK 467


Lambda     K      H
   0.317    0.134    0.391 

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: 572
Number of extensions: 31
Number of successful extensions: 3
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: 477
Length of database: 474
Length adjustment: 33
Effective length of query: 444
Effective length of database: 441
Effective search space:   195804
Effective search space used:   195804
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: 51 (24.3 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