GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Klebsiella michiganensis M5al

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BWI76_RS02800 BWI76_RS02800 ABC transporter

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS02800
          Length = 500

 Score =  157 bits (397), Expect = 4e-43
 Identities = 91/246 (36%), Positives = 143/246 (58%), Gaps = 9/246 (3%)

Query: 4   EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63
           + IL   GL K +  V ALD  +F L  GEI+A++G+NGAGKS++IKA++G    D G I
Sbjct: 7   QEILRTEGLSKFFPGVKALDNVNFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGAI 66

Query: 64  RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123
            LEG+ I  ++   A+Q GI TVYQ + L P +S+ADN+F+GRE R+ G+       L R
Sbjct: 67  WLEGREISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPRRFGL-------LQR 119

Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183
             MEK+A A ++  G     ++ + +   S   +Q VA+ RA    +KV+I+DEPTA+L 
Sbjct: 120 KEMEKRATALMASYGFSL--DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLD 177

Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243
            +E   +  L+  +R  G+ ++ ++H +  V+ V+DRI + R G  +     ++    + 
Sbjct: 178 TQEVEMLFTLMRQLRDSGVSLIFVTHFLDQVYAVSDRITVLRNGGFVGCRETRELPQIEL 237

Query: 244 VAFMTG 249
           V  M G
Sbjct: 238 VKMMLG 243



 Score = 84.7 bits (208), Expect = 3e-21
 Identities = 58/213 (27%), Positives = 105/213 (49%), Gaps = 9/213 (4%)

Query: 16  YGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSP 75
           +G+   +   +  + PGEI+ + G  G+G++   + I G    D G+  ++GKP   RSP
Sbjct: 270 FGKKGTIAPFNLQVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGKAWIKGKPQTLRSP 329

Query: 76  MEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARA 132
            +A   GI    ++     +  A S+ +N+ L  + ++      W R + R    + A  
Sbjct: 330 HQASCLGIGFCPEDRKTDGIIAAASVRENIVLALQAQRG-----WLRPISRREQNEIAER 384

Query: 133 KLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLE 192
            + +LG+ T  +  Q +E LSGG +Q V ++R      + +I+DEPT  + V     ++ 
Sbjct: 385 FIRQLGIRT-PSAEQPIEFLSGGNQQKVLLSRWLLTKPQFLILDEPTRGIDVGAHAEIIR 443

Query: 193 LILDVRRRGLPIVLISHNMPHVFEVADRIHIHR 225
           LI  +   GL +++IS  +  +   ADR+ I R
Sbjct: 444 LIETLCADGLALLVISSELEELVGYADRVIIMR 476


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: 294
Number of extensions: 11
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: 500
Length adjustment: 29
Effective length of query: 231
Effective length of database: 471
Effective search space:   108801
Effective search space used:   108801
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