GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Sphingomonas koreensis DSMZ 15582

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ga0059261_2556 Ga0059261_2556 ABC-type multidrug transport system, ATPase component

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Korea:Ga0059261_2556
          Length = 587

 Score = 92.4 bits (228), Expect = 2e-23
 Identities = 53/175 (30%), Positives = 97/175 (55%), Gaps = 2/175 (1%)

Query: 22  IQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYLGKSIKGKGAWDL 81
           + A+  +   ++ G +  L+G +GAGKTT ++ I G L+   G +         +G  D 
Sbjct: 23  VVAIDDLSASIKTGIITGLVGPDGAGKTTLIRMIAGLLTPTRGKLTVNDLEPASQG--DA 80

Query: 82  VKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTIFPRLRERKDQLAG 141
           +++ L  +P+  G++  +T+ ENL + + +R       AD+ +    F  L+   ++ AG
Sbjct: 81  LRQQLGYMPQRFGLYEDLTVLENLTLYSDLRGVDPAKRADMFERMLEFTDLKRFTERRAG 140

Query: 142 TMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDVYALGVTIV 196
            +SGG +Q L +   L+  P+VLLLDEPS+G+ PI   +++++V D+   G TI+
Sbjct: 141 KLSGGMKQKLGLACTLLGDPQVLLLDEPSVGVDPISRRELWKMVGDLAGEGKTII 195



 Score = 87.8 bits (216), Expect = 4e-22
 Identities = 63/228 (27%), Positives = 113/228 (49%), Gaps = 21/228 (9%)

Query: 3   EKSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMN 62
           E + +V+++ K L   +G   A   V F+V+ GE+  L+G NGAGK+TT K + G L  +
Sbjct: 329 EAAGEVVIEAKHLTKRFGDFAATDDVSFDVKRGEIYGLLGPNGAGKSTTFKMLCGLLVPS 388

Query: 63  DGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYI-------RKDK 115
            G+   LG S+K +   D  ++ L  + +   ++  +++ +N++  A I       R+++
Sbjct: 389 SGDANVLGYSLK-RSPGD-ARQRLGYMAQKFSLYGTLSVRQNMEFFAGIYGLDGSDRRER 446

Query: 116 AGILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSP 175
              + D    F + P L    D L      G +Q LA+  A+M  P +L LDEP+ G+ P
Sbjct: 447 IDAMID---AFALKPYLAMSPDAL----PLGFKQRLALACAIMHDPAILFLDEPTSGVDP 499

Query: 176 IMVDKIFEVVRDVYALGVTIVLVEQNASRA-----LAIADRGYVMESG 218
           +   + +  +  V   GVT+++       A     + +  RG ++ SG
Sbjct: 500 LTRREFWTHINGVVEKGVTVMVTTHFMDEAEYCDRIGLIYRGKLIASG 547


Lambda     K      H
   0.317    0.136    0.373 

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: 340
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 242
Length of database: 587
Length adjustment: 30
Effective length of query: 212
Effective length of database: 557
Effective search space:   118084
Effective search space used:   118084
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: 50 (23.9 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