GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Azospirillum brasilense Sp245

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  159 bits (403), Expect = 9e-44
 Identities = 97/248 (39%), Positives = 145/248 (58%), Gaps = 9/248 (3%)

Query: 2   AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61
           A  P+L  RGL K +  V ALD  DF +  GEI A++G+NGAGKS++IK ++G    D G
Sbjct: 8   ASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAG 67

Query: 62  EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121
            + LEG+ I  R   EA++  I TVYQ + L P LS+A+N+FLGR+  + G+       +
Sbjct: 68  TVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGL-------V 120

Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181
           DR AM ++ARA L   GL    ++   +   S   +Q VA+ARA    +KV+I+DEPTA+
Sbjct: 121 DRGAMRRRARAVLIPYGLTL--DVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTAS 178

Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241
           L  +E   + +++  +R RG+ IV ++H +  V+ + DRI + R GR +      +    
Sbjct: 179 LDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRL 238

Query: 242 DAVAFMTG 249
           D VA M G
Sbjct: 239 DLVAMMLG 246



 Score = 92.4 bits (228), Expect = 2e-23
 Identities = 61/255 (23%), Positives = 124/255 (48%), Gaps = 13/255 (5%)

Query: 2   AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61
           A+ P++  RG    YG+  +++  D D+ PGE++ + G  G+G++   + + G    D G
Sbjct: 267 ARPPLVRFRG----YGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRG 322

Query: 62  EIRLEGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWF 118
           E  ++G+ ++ R P +A + G     ++     +  ALS+ +N+ L  + R+      W 
Sbjct: 323 EAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQ-----GWL 377

Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEP 178
           R + R   E+ A   +  L + T  +  Q ++ LSGG +Q   +AR  A   +++I+DEP
Sbjct: 378 RPIPRCRQEEIADRFIRLLDIRT-PHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEP 436

Query: 179 TAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDY 238
           T  + V     ++ LI  +   G+ ++++S  +  +   + R+ + R  R +  +   + 
Sbjct: 437 TRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEV 496

Query: 239 TMSDAVAFMTGAKEP 253
            +   VA +     P
Sbjct: 497 AVDRIVAAIASESVP 511


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: 334
Number of extensions: 21
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: 516
Length adjustment: 29
Effective length of query: 231
Effective length of database: 487
Effective search space:   112497
Effective search space used:   112497
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