GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c07320 in Phaeobacter inhibens BS107

Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= reanno::Phaeo:GFF717
         (261 letters)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          Length = 503

 Score =  166 bits (420), Expect = 9e-46
 Identities = 88/246 (35%), Positives = 142/246 (57%), Gaps = 4/246 (1%)

Query: 1   MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60
           M+   P++R++GI K F  V AL GVS+ + PGE H L+G+NGAGKST +K + G+H+P 
Sbjct: 1   MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60

Query: 61  KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120
           +G I+   QP+  + P DA A GI  +HQ L++   +SV+ N ++G  P ++ G +   +
Sbjct: 61  EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120

Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180
            +      +E++ K+G N +     VG LS   +Q V IARA+   AK +I DEPT++L 
Sbjct: 121 LEAKTNAILEKL-KVGFNAK---TRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLT 176

Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
             +   +   I  +++QGV + +I+H +     + DR +VL  G+  GT    + + E +
Sbjct: 177 DAEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENV 236

Query: 241 QDMMAG 246
             MM G
Sbjct: 237 TQMMIG 242



 Score = 91.3 bits (225), Expect = 4e-23
 Identities = 66/225 (29%), Positives = 104/225 (46%), Gaps = 7/225 (3%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85
           V+ +V  GE     G  GAG++   +T+ G+  PT G I  +G  +    P DAI  GI+
Sbjct: 275 VNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGIS 334

Query: 86  TVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMR-KMGINLRG 141
            V +      ++  M+   N  +      K GP   F  D A     ++ R K+ I   G
Sbjct: 335 LVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGP---FVADGAEIAIFDQYRDKLDIRTPG 391

Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201
             Q VG LSGG +Q + I + +     VLI+DEPT  + V   A +   +  +  QG AV
Sbjct: 392 WKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAV 451

Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
           + I+  +   L V DR   +  G+ + T    +++ E L   ++G
Sbjct: 452 IVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496


Lambda     K      H
   0.321    0.137    0.395 

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: 309
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 503
Length adjustment: 29
Effective length of query: 232
Effective length of database: 474
Effective search space:   109968
Effective search space used:   109968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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 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