GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF2860 HP15_2804 oligopeptide/dipeptide
           ABC transporter, ATP-binding protein-like protein
          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 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