GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Azospirillum brasilense Sp245

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate AZOBR_RS33725 AZOBR_RS33725 phosphomannomutase

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__azobra:AZOBR_RS33725
          Length = 468

 Score =  167 bits (423), Expect = 7e-46
 Identities = 140/459 (30%), Positives = 211/459 (45%), Gaps = 38/459 (8%)

Query: 9   IRGTLWEKVTPELAMKVGMAVGTY---KSGK-ALVGRDGRTSSVMLKNAMISGLLSTGME 64
           IRG +   +T   A  VG A GT    K G  A +G DGR SS  L+ A++ GL+STG+ 
Sbjct: 17  IRGIVGTTLTTADARAVGRAFGTMIVRKGGTTACIGYDGRHSSPELEEALVDGLVSTGLR 76

Query: 65  VLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEI 123
           V    L PTP L + TR + AD G+MIT SHNPP  NG+K+  G G   Y    + L  I
Sbjct: 77  VTRIGLGPTPMLYFATRDREADGGIMITGSHNPPEYNGIKMMLGKGP-VYGAMIQELGAI 135

Query: 124 IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLR 183
             +G++             V+V   Y+  +L       +LK+ +D  NGA   +   L  
Sbjct: 136 AAAGDYATGAGS----AERVDVQDAYVARLLKDYDGVRDLKIAWDAGNGATGEILRRLTA 191

Query: 184 EMGAKVLSVNAHVDGHFPGRKPEPRYE-NIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242
            +  + + +   +DG FP   P+P  E N+  L K V E G D+ I  DGD DRI   D 
Sbjct: 192 TLPGEHILLFDAIDGDFPNHHPDPTVEKNLVDLKKAVAEHGCDIGIGFDGDGDRIGAIDH 251

Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302
            G  V  D ++A++A   ++ H G T++  +     +   + R GG+ +    G  H  +
Sbjct: 252 LGRVVWGDQLVAIYAADVLKSHPGATIIADVKASQTLFDEIARLGGQPLMWKTG--HSLL 309

Query: 303 KRYKA-------------IFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDENGPLSELVK 349
           K   A             IF A+ W      +G     +  + L+ ++    GPL+ L  
Sbjct: 310 KAKMAETGSPLAGEMSGHIFFADKW------YGFDDALYCAVRLIGQVSRSGGPLAALRD 363

Query: 350 EIP-TYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILI 408
            +P      +      +E K +VVR    EV+ +L +E  +V  I G R+   DG W L+
Sbjct: 364 RLPEVINTPETRFQADEERKFQVVR----EVKERLKAEGAQVNDIDGVRVQTPDG-WWLL 418

Query: 409 RPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEA 447
           R S T+  +   AE+ T+   + L  M  + +     EA
Sbjct: 419 RASNTQDVLVARAESSTQDGLERLKSMVVAQLEASGLEA 457


Lambda     K      H
   0.318    0.138    0.402 

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: 537
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 450
Length of database: 468
Length adjustment: 33
Effective length of query: 417
Effective length of database: 435
Effective search space:   181395
Effective search space used:   181395
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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