GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Pseudomonas fluorescens FW300-N2E2

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456
          Length = 518

 Score =  338 bits (866), Expect = 4e-97
 Identities = 196/501 (39%), Positives = 307/501 (61%), Gaps = 14/501 (2%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTT--GSVV 65
           L   GI KTF GVKAL  I      G+   L GENGAGKSTL+K+LS  Y   T  G ++
Sbjct: 6   LQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEIL 65

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYEA 124
            +GQ +     +    AG+ II+QEL LVP+++VAENI++G +L   GG +N   + + A
Sbjct: 66  WDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHRA 125

Query: 125 GLQLKHLGM-DIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
              ++ L + D++   P+     G  Q+VEIAKAL + A+++  DEP+S+L+  EI+ L 
Sbjct: 126 EALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVLL 185

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
            +IR+L+ +G   +Y+SH+++E+ A+ D I+V +DG+++ T T M  +    ++  MVGR
Sbjct: 186 DIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIAT-TAMADMSIPKIITQMVGR 244

Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTP-------ISLAVRSGEIVGLFGLVGAGRS 296
           ++ ++Y  +P   GE            V  P       IS  ++ GEI+G+ GLVGAGR+
Sbjct: 245 EMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAGRT 304

Query: 297 ELMKGMFGGTQIT-AGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNI 355
           EL+  +FG       G+V+++ Q ID R P  +I AG+ + PEDRK +GIIP   V  NI
Sbjct: 305 ELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQNI 364

Query: 356 NISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLS 415
            ++    +      I+   E  + D  I  +++KT      I +LSGGNQQKA+L + L 
Sbjct: 365 TLAVLDNYSKL-TRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLAKMLL 423

Query: 416 EEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREG 475
            + +V++LDEPTRG+DVGAK+EIY ++ ALAA+GV+++  SS+L EVLGV+DR++V+ +G
Sbjct: 424 TKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGDG 483

Query: 476 EIAGELLHEQADERQALSLAM 496
           ++ G+ ++ +  + Q L+ A+
Sbjct: 484 QLRGDFINHELTQEQVLAAAL 504


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: 715
Number of extensions: 49
Number of successful extensions: 12
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: 518
Length adjustment: 35
Effective length of query: 469
Effective length of database: 483
Effective search space:   226527
Effective search space used:   226527
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 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