GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Phyllobacterium brassicacearum STM 196

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_106713881.1 CU102_RS25520 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_003010955.1:WP_106713881.1
          Length = 512

 Score =  361 bits (927), Expect = e-104
 Identities = 207/493 (41%), Positives = 298/493 (60%), Gaps = 9/493 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           LS  GI K F G+ AL+  SF    G+VHAL+G+NGAGKSTL+K+L+G Y    G V  +
Sbjct: 7   LSMTGIDKRFAGIPALSGASFAVGRGEVHALIGQNGAGKSTLIKVLTGYYRRDAGDVAFD 66

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G+         A  +G++ IYQE++LVP  ++ ENI LG+     G+++   ++ EA   
Sbjct: 67  GKPFEVFSPQLAQASGISTIYQEINLVPYRSITENICLGREARHYGLLDWKRMHKEAETL 126

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
           L+   + +D D PL   +    QMV IA+A+  +AK++  DEPTSSL  RE+  LF VIR
Sbjct: 127 LRRFNVRVDVDRPLMEFNTATQQMVAIARAIGFSAKLVVMDEPTSSLDDREVTVLFDVIR 186

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247
           +L++EG  +++VSH+++E++ + D +T+ +DGR VKT   M ++D   LV +M+GR I  
Sbjct: 187 QLKQEGVSVVFVSHKLDELYEVCDRVTIMRDGRTVKT-AAMTEIDKIGLVSSMLGRTINR 245

Query: 248 IYGW-------QPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300
             G          +  G+  L    +        +S  VRSGEI G  GL+GAGR+E  +
Sbjct: 246 AEGHATAFSDRDEKKIGKVLLSAQNLSINRTVQDVSFDVRSGEIAGFAGLLGAGRTETAR 305

Query: 301 GMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360
            +FG  +  AG ++ D Q  D R P+ AIAAGM  C EDRK+EGI+P  SV +N+ ++  
Sbjct: 306 LVFGIDRPRAGIMHYDGQQFDPRSPADAIAAGMGFCTEDRKSEGIVPEMSVAENMMLALM 365

Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420
            K    G VI+   +    +  IR L+IK  G +Q +  LSGGNQQK +LGRWL+    +
Sbjct: 366 PKVSKSG-VIDEKAQRKIVERFIRQLDIKCSGPDQKVRELSGGNQQKVLLGRWLAMNPTL 424

Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480
           ++LDEPTRGIDVGAK EI ++I +LA +G+AVL  SS+L EV+  ADR+ V+REG    E
Sbjct: 425 LILDEPTRGIDVGAKGEIQSLIKSLADRGLAVLMISSELEEVIEGADRVFVLREGITVAE 484

Query: 481 LLHEQADERQALS 493
               QA E   +S
Sbjct: 485 FDRNQATEDVLMS 497


Lambda     K      H
   0.319    0.136    0.391 

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: 619
Number of extensions: 31
Number of successful extensions: 9
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: 504
Length of database: 512
Length adjustment: 34
Effective length of query: 470
Effective length of database: 478
Effective search space:   224660
Effective search space used:   224660
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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