GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Marinobacter adhaerens HP15

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  110 bits (276), Expect = 6e-29
 Identities = 75/234 (32%), Positives = 120/234 (51%), Gaps = 11/234 (4%)

Query: 10  RGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP 69
           RG+  +   + ALD     L  GE+LA++G++G GK+++ + I G   P  G + L G+ 
Sbjct: 366 RGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAPSTGSVTLNGQR 425

Query: 70  IQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQ 129
           I+   PM+ R   I+ ++Q+    P  S+     +G  I KP     +   +     + Q
Sbjct: 426 IENLPPMD-RARMIQPIFQD----PYSSLNPRKTIGEIIAKP----LFVHGIGSNQEQHQ 476

Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189
              K+ EL  +  +  N   + LSGGQRQ  A+ RA     +VVI DEPT+AL V    +
Sbjct: 477 QVRKMMELVGLPSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQ 536

Query: 190 VLELILDVR-RRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242
           +L L+LD+R    L  + ++HN+  V  +ADR+ +  LG  +     +D  MSD
Sbjct: 537 ILNLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLG-EIVECGERDQVMSD 589



 Score = 68.2 bits (165), Expect = 4e-16
 Identities = 57/210 (27%), Positives = 100/210 (47%), Gaps = 17/210 (8%)

Query: 28  DLYPGEILAVIGDNGAGKSSMIKAISGAVTP----DEGEIRLEGKPIQFRSPME----AR 79
           +L  GE L ++G++G+GKS    A+   + P        I  +G  +   +  E     R
Sbjct: 32  ELNRGETLGIVGESGSGKSMTALALMNLLPPAAKRQASCIDFDGSDLTHATERELASKIR 91

Query: 80  QAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139
              I  ++Q     P  S+     +GR++++   +    R +     E +A   L ++GL
Sbjct: 92  GQRIGMIFQ----EPMTSLNPVYSIGRQLKETMTL---HRKVSDTEAENRAVYLLEKVGL 144

Query: 140 M-TIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVR 198
                 + Q    LSGGQRQ V +A A     +++I DEPT AL V    ++L L+ +++
Sbjct: 145 PDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIADEPTTALDVTIQAQILHLLRELQ 204

Query: 199 RR-GLPIVLISHNMPHVFEVADRIHIHRLG 227
           +  G+ ++LI+H++  V   AD I +   G
Sbjct: 205 QEFGMSMILITHDLGVVSRAADNIAVMYAG 234


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: 388
Number of extensions: 20
Number of successful extensions: 5
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: 672
Length adjustment: 31
Effective length of query: 229
Effective length of database: 641
Effective search space:   146789
Effective search space used:   146789
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: 50 (23.9 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