GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Acidovorax sp. GW101-3H11

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ac3H11_1109 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1109
          Length = 513

 Score =  139 bits (350), Expect = 1e-37
 Identities = 86/246 (34%), Positives = 134/246 (54%), Gaps = 13/246 (5%)

Query: 11  GLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPI 70
           G+ KRY  V A       + PGEI AV+G+NGAGKS+++K I G+V PDEG +   G+ +
Sbjct: 2   GITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAV 61

Query: 71  QFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQA 130
           Q R+P EAR  GI  V+Q+ +L   L++A+N++LG +           +SL  A + ++ 
Sbjct: 62  QVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLD-----------KSLTLAEVTQRI 110

Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190
            AK +E GL  I  + + V TLS G+ Q V + RA     KV+I+DEPT+ L  +   ++
Sbjct: 111 SAKAAEYGL-DIDPL-RPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKL 168

Query: 191 LELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGA 250
             ++  +   G  I+ ISH +  +  +     + R G+   V NP + T +     M GA
Sbjct: 169 FVVLRKLASEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGA 228

Query: 251 KEPPRE 256
           + P  E
Sbjct: 229 EPPALE 234



 Score = 70.9 bits (172), Expect = 5e-17
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 12/250 (4%)

Query: 6   ILTARGLVKRYGRVTALDRAD--FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE-GE 62
           +L  +GL         +D  D  F++  GE++ + G +G G+  ++ A+SG     E   
Sbjct: 244 VLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGEDQRAEPAS 303

Query: 63  IRLEGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFR 119
           I++ G+      P + R  G+  V +        P + +A N+ L R+    G    W +
Sbjct: 304 IQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAVGG--SGWIK 361

Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179
                A++K A   +    +      + A ++LSGG  Q   V R      K++I+ +PT
Sbjct: 362 V---GALQKHAEDIIQRFNVKA-GGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQPT 417

Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239
             + V  + ++   IL +R  G  ++++S  +  +FE+ DR+H+   GR    +   + T
Sbjct: 418 WGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEAT 477

Query: 240 MSDAVAFMTG 249
           +     +M+G
Sbjct: 478 VERIGEWMSG 487


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: 271
Number of extensions: 15
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: 513
Length adjustment: 29
Effective length of query: 231
Effective length of database: 484
Effective search space:   111804
Effective search space used:   111804
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.

Links

Downloads

Related tools

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