GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Phaeobacter inhibens BS107

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  151 bits (382), Expect = 2e-41
 Identities = 89/249 (35%), Positives = 139/249 (55%), Gaps = 8/249 (3%)

Query: 3   QEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62
           Q P+L   G+VK +  V ALD     + PGE+ A++G+NGAGKS+++K + G   PDEG+
Sbjct: 4   QSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQ 63

Query: 63  IRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122
           I +  +P+    P++A+  GI  ++Q L+L+  LS+A+N++LG   RK       F  +D
Sbjct: 64  IIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKR------FGLVD 117

Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182
            A +E +  A L +L +    N    V  LS   +Q V +ARA    +K VI DEPTA+L
Sbjct: 118 WAELEAKTNAILEKLKVGF--NAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASL 175

Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242
              E   + E+I D++ +G+ I  ISH M  +F++ DRI + R G+    +N  +    +
Sbjct: 176 TDAEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEEN 235

Query: 243 AVAFMTGAK 251
               M G K
Sbjct: 236 VTQMMIGRK 244



 Score = 85.1 bits (209), Expect = 3e-21
 Identities = 62/227 (27%), Positives = 106/227 (46%), Gaps = 9/227 (3%)

Query: 26  DFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIET 85
           +F++  GE++   G  GAG++ + + + G   P  G I L+G  +   SP +A + GI  
Sbjct: 276 NFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISL 335

Query: 86  VYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTI 142
           V ++     L   ++  DNM L +        G +       A+  Q R KL     +  
Sbjct: 336 VPEDRKGQGLVLGMNCRDNMTLPQVDDLKA--GPFVADGAEIAIFDQYRDKLD----IRT 389

Query: 143 QNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGL 202
               Q V  LSGG +Q + + +  +    V+I+DEPT  + V     +  L+ D+  +G 
Sbjct: 390 PGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGY 449

Query: 203 PIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249
            +++IS  MP V  VADRI     GR +     ++ T  + +A ++G
Sbjct: 450 AVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496


Lambda     K      H
   0.321    0.136    0.383 

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: 280
Number of extensions: 17
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: 260
Length of database: 503
Length adjustment: 29
Effective length of query: 231
Effective length of database: 474
Effective search space:   109494
Effective search space used:   109494
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 (21.8 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