Aligments for a candidate for xacF in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments for a candidate for xacF 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)



>lcl|FitnessBrowser__Korea:Ga0059261_3374 Ga0059261_3374
           NAD-dependent aldehyde dehydrogenases
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources