GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2274
          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:

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