GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Desulfoscipio geothermicus DSM 3669

Align TRAP-type large permease component (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease

Query= uniprot:Q930R2
         (425 letters)



>NCBI__GCF_900115975.1:WP_092484450.1
          Length = 425

 Score =  328 bits (840), Expect = 3e-94
 Identities = 166/416 (39%), Positives = 256/416 (61%), Gaps = 1/416 (0%)

Query: 1   MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60
           M+L++F  S    + IGVPVAFSL    +  + Y G     +  Q +  G D+F L+AIP
Sbjct: 1   MSLILF-ASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDSFPLMAIP 59

Query: 61  FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120
           FF++AG LMN GG+SRR++DFA A VGH  GGL  V  MA+++ A++SGS AA TAA+  
Sbjct: 60  FFMMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGG 119

Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180
           ++IP + K GY    ++ L A+ G +  VIPPS+ F++FG  + VSI +LF+AGIVPG++
Sbjct: 120 MMIPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSGVSIAELFLAGIVPGVL 179

Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240
           + + L+     +V+        R P KE V     AL AL MP IILGGI +G  TPTEA
Sbjct: 180 IAVLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEA 239

Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300
           AV+A VY   VG+ +YREL   ++   +  A  + AV++ L+  A   SW++ +  IP +
Sbjct: 240 AVIAVVYGFIVGIFVYRELNLANIMEAMKDAVISNAVVLMLLAFASTFSWIMASELIPQK 299

Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360
           I   +S +     + + ++ + +L++GT L+ TP +++L P+L+P+ +   ++ V+FGVL
Sbjct: 300 IAALMSSIAPNQFIFLLLVTVFLLIIGTFLETTPALILLVPILVPVAQTFDVNLVHFGVL 359

Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416
            ++N  IG++TPP+G+ L V S + +VPL  +   + PF++  I  L +L   P I
Sbjct: 360 MVVNLAIGMVTPPLGITLFVASNISKVPLANLFRAIVPFILCMIAALLVLTFVPQI 415


Lambda     K      H
   0.331    0.145    0.430 

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: 484
Number of extensions: 23
Number of successful extensions: 1
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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