GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Pseudomonas simiae WCS417

Align TRAP-type large permease component (characterized, see rationale)
to candidate GFF3396 PS417_17380 membrane protein

Query= uniprot:Q930R2
         (425 letters)



>FitnessBrowser__WCS417:GFF3396
          Length = 426

 Score =  303 bits (775), Expect = 9e-87
 Identities = 159/416 (38%), Positives = 258/416 (62%), Gaps = 3/416 (0%)

Query: 1   MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60
           M  ++ + S +  + IG+PVA++L    ++  W++ +    ++ Q +  G + F+L+AIP
Sbjct: 1   MDALILLGSFIALILIGMPVAYALGLSALIGAWWIDIPFQALMIQ-VAGGVNKFSLMAIP 59

Query: 61  FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120
           FF+LAG +M  GG+SRR++ FA   VG +RGGL +V IMA+    +ISGS+ ADTA++ +
Sbjct: 60  FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119

Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAA--NVSITQLFMAGIVPG 178
           +LIP M + GY    +  +  +G V A + PPS   +++ +AA  +VSI  LFMAG+VPG
Sbjct: 120 VLIPEMERRGYPREFATAVTVSGSVQALLTPPSHNSVLYSLAAGGSVSIASLFMAGVVPG 179

Query: 179 LIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPT 238
           L+M   L+   L+  +K +       P+K+ +     ALW L   VIILGGI +G+ T T
Sbjct: 180 LLMSACLMVLCLIFAKKRNYPKGEVIPLKQALKICADALWGLMAMVIILGGILSGIFTAT 239

Query: 239 EAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIP 298
           E+A +A ++A FV M IYR+ K  +LP ++ +  +T +++M L+  A    +++T   IP
Sbjct: 240 ESAAIAVLWAFFVTMFIYRDYKWSELPKLMHRTVRTISIVMILIAFAASFGYIMTLMQIP 299

Query: 299 SEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFG 358
           ++IT     L D   +++  I  ++L++GT +D+ P ILILTP+L+P++   G+DPV+FG
Sbjct: 300 AKITTLFLTLSDNRYVILMCINAMLLLLGTVMDMAPLILILTPILLPVVLGIGVDPVHFG 359

Query: 359 VLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFP 414
           ++ ++N  IGL+TPPVG VL V + VG+V + K +  + PF     LVL  +   P
Sbjct: 360 MIMLVNLGIGLITPPVGAVLFVGAAVGKVSIEKTVKALLPFYGVLFLVLMAVTYIP 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: 463
Number of extensions: 22
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: 425
Length of database: 426
Length adjustment: 32
Effective length of query: 393
Effective length of database: 394
Effective search space:   154842
Effective search space used:   154842
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 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