GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456
          Length = 518

 Score =  361 bits (927), Expect = e-104
 Identities = 212/501 (42%), Positives = 312/501 (62%), Gaps = 13/501 (2%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDI 79
           ++ +  + K F GV AL+    ++  GE   L GENGAGKSTLMK+LS VY   +  G+I
Sbjct: 5   LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEI 64

Query: 80  LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139
           L DG+P++     + +A GI IIHQEL L+  LS A+NIF+G E     G  ++   +  
Sbjct: 65  LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGR-MNYPAMIH 123

Query: 140 QAAAIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
           +A A+   +++ DM+ S PV +     QQ+VEIAKAL+  +R+LI+DEP++AL  +EI  
Sbjct: 124 RAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEV 183

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           L  IIRDL+A+GV  VYISHK+DE+  + D +SV+RDGK+IAT  M + S+  II+ MVG
Sbjct: 184 LLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMVG 243

Query: 259 RALDGEQRIPPDTSRNDVVLEVRGLN-------RGRAIRDVSFTLRKGEILGFAGLMGAG 311
           R +       P     +V+ E R          R + + D+SF L++GEILG AGL+GAG
Sbjct: 244 REMSNLYPTEPHDV-GEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAG 302

Query: 312 RTEVARAIFGADPLE-AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370
           RTE+  A+FGA P    GE+ ++G +   ++P  ++  G+  + EDRK  G+   + V  
Sbjct: 303 RTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQ 362

Query: 371 NIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430
           NI L+ +  ++++  +D  A   +    + ++ +KT S       LSGGNQQK V+AK L
Sbjct: 363 NITLAVLDNYSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLAKML 422

Query: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490
           L    +L  DEPTRG+DVGAK EIYKL+ ALA +G +I+M+SSEL EVL +S RVLV+ +
Sbjct: 423 LTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGD 482

Query: 491 GRITGELARADATQEKIMQLA 511
           G++ G+    + TQE+++  A
Sbjct: 483 GQLRGDFINHELTQEQVLAAA 503



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 69/253 (27%), Positives = 118/253 (46%), Gaps = 20/253 (7%)

Query: 274 NDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA-- 327
           +D +L++ G+ +     +A+  +   +R GE +G  G  GAG++ + + +    P     
Sbjct: 2   SDYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWD 61

Query: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRV--GF 385
           GEI+  G     +S ++  A GI  + ++     L   + V  NI    MG    +  G 
Sbjct: 62  GEILWDGQPLKAQSISETEAAGIVIIHQE---LTLVPDLSVAENIF---MGHELTLPGGR 115

Query: 386 MDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445
           M+  A+   A+  +R+L +   +V        GG QQ + IAK L +   +L  DEP+  
Sbjct: 116 MNYPAMIHRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSA 175

Query: 446 IDVGAKSEIYKLLDALAE---QGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADA 502
           +    +SEI  LLD + +   +G A V IS +L EV  +   + V+ +G+     A AD 
Sbjct: 176 L---TRSEIEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADM 232

Query: 503 TQEKIMQLATQRE 515
           +  KI+     RE
Sbjct: 233 SIPKIITQMVGRE 245


Lambda     K      H
   0.320    0.135    0.372 

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: 637
Number of extensions: 35
Number of successful extensions: 8
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: 520
Length of database: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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: 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