GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Tistlia consotensis USBA 355

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  350 bits (898), Expect = e-101
 Identities = 193/501 (38%), Positives = 292/501 (58%), Gaps = 4/501 (0%)

Query: 14  GVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKII 73
           G    A P+    LLE+  VS+ FPGV+AL  V  ++RPG V  L GENGAGKST++ +I
Sbjct: 10  GPSDRAAPLPAAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMI 69

Query: 74  AGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGF 133
           AG  +P  GE R RG+PV  ++   A   GI+ + QE +L+P M++ EN+++G E     
Sbjct: 70  AGALRPSEGEFRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR-L 128

Query: 134 HMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTS 193
            ++D R +H     +L+RL   L P ++V +L+ AE+QMVEIAKA   +  +LI+DEPT+
Sbjct: 129 GLLDRRALHDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTA 188

Query: 194 AITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDG 253
           ++T++E A LF +I  +KAQG G+IYITH+++E+  I D + V RDG Y+    A +   
Sbjct: 189 SLTERETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPE 248

Query: 254 DSLISMMVGRELSQLFP-VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMG 312
             L+ +M GR   +LFP VR KP  +LL   R     G     S  + AGEI+G+AGL+G
Sbjct: 249 GELVRLMTGRVYDELFPKVRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVG 308

Query: 313 SGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVL 372
           SG++ VA A FG+     G + L G+ V    P   +++GF  +  DR+  GL     V 
Sbjct: 309 SGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVR 368

Query: 373 ENMEM--AVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLA 430
           EN+ +    L  +     + ++        + ++L ++ P +E+ ++  SGGNQQK LLA
Sbjct: 369 ENVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLA 428

Query: 431 RWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMV 490
           +      ++   DEPT G+DVG +  IY  I  L   G  +++ISS+LPEVL +S+R  V
Sbjct: 429 KSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYV 488

Query: 491 MHEGDLMGTLDRSEATQERVM 511
            + G +   L   E T+E+V+
Sbjct: 489 FYRGRVQAELAGDEITEEKVL 509



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 56/222 (25%), Positives = 109/222 (49%), Gaps = 6/222 (2%)

Query: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354
           V F L  GE+  + G  G+G++ +   I G      GE    G+PV ++  H A   G +
Sbjct: 42  VDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRFRGEPVELNSVHHARGLGIS 101

Query: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414
            + ++     L P ++V EN+ +         G + ++AL    + + K+L       ++
Sbjct: 102 AVFQE---FSLVPQMTVEENLFLGA--ESTRLGLLDRRALHDRADAILKRLGFPLRPRDR 156

Query: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474
            +  L+   QQ   +A+   +   +LILDEPT  +     A++++LI  + ++G+ VI I
Sbjct: 157 VLH-LTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLIEQVKAQGVGVIYI 215

Query: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516
           +  L E+  + DR+ V+ +G  + T+D     +  +++L +G
Sbjct: 216 THRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTG 257



 Score = 68.6 bits (166), Expect = 5e-16
 Identities = 61/245 (24%), Positives = 109/245 (44%), Gaps = 11/245 (4%)

Query: 29  EIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRG 88
           E+++V +      ++ +  L V  G ++ L G  G+GKS + +   G+ +   G +RL+G
Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333

Query: 89  KPVTFDTPLAALQAGIAMI---HQELNLMPHMSIAENIWIGREQLNGFH---MIDHREMH 142
           + VT   P   L+ G   +    ++  LM    + EN+ +    L  F    ++D R   
Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGET 393

Query: 143 RCTAQLLERLRINLDP---EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKE 199
               +L E+L  NL P   E  V   S   +Q V +AK+ +    +   DEPT  +    
Sbjct: 394 DRVRRLAEQL--NLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGT 451

Query: 200 VAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISM 259
              ++  I DL   G GI+ I+  + EV ++++   VF  G        D +  + ++S 
Sbjct: 452 RVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGDEITEEKVLSH 511

Query: 260 MVGRE 264
              R+
Sbjct: 512 FFERD 516


Lambda     K      H
   0.321    0.137    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: 641
Number of extensions: 25
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 518
Length adjustment: 35
Effective length of query: 486
Effective length of database: 483
Effective search space:   234738
Effective search space used:   234738
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 Apr 09 2024. 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