GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Rhizobium freirei PRF 81

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate WP_004129793.1 RHSP_RS32525 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000359745.1:WP_004129793.1
          Length = 527

 Score =  365 bits (938), Expect = e-105
 Identities = 208/482 (43%), Positives = 305/482 (63%), Gaps = 15/482 (3%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           V KSF GV AL  V L +  G +HAL+GENGAGKSTL+KIL        G++   G+ + 
Sbjct: 18  VRKSFGGVHALRGVSLTIQPGTIHALVGENGAGKSTLLKILQGVVTPTEGSIEVFGEHMS 77

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLG-LVDWSRLRADAQALLND 127
              +P   ++LGI  I+Q+ +L P L+VA+N++L REPRRL  LVD  R  A A  ++  
Sbjct: 78  S-SSPENSRRLGIEMIFQDLSLIPTLTVAQNIFLNREPRRLSILVDERREIAQAAEIIGQ 136

Query: 128 LGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187
           L L ++P  PV  L+  + Q+ EIAKA+  +AR++I+DEPT++LS +E D L  ++  L 
Sbjct: 137 LNLRVDPRTPVFELSPGQAQLTEIAKAIHQDARILILDEPTSSLSAQEADTLFGMLKKLT 196

Query: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV---EFE 244
           A   +VIYVSHR+ E+  + D  T++RDG+ V SG  ++  +  +V+ MVG+ V   +++
Sbjct: 197 AAGTAVIYVSHRMSEIMTIADEITILRDGQNVTSGKTSEFTLDSIVQHMVGKRVTGFQYQ 256

Query: 245 RRKRRRPPGAVVLKVEGVTPAAPRLSAP-GYLRQVSFAARGGEIVGLAGLVGAGRTDLAR 303
            R   R  G   L V G       LS P G    VSF    GEIVG+AGL+GAGR++LAR
Sbjct: 257 ARAIDRS-GKPALSVRG-------LSGPSGKPSDVSFDVHRGEIVGIAGLMGAGRSELAR 308

Query: 304 LIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSL 363
           L+FG D   AG V + D  +  +SP DAI+AGI+LVPE R ++G  ++HS+  NL LP +
Sbjct: 309 LLFGVDKKTAGTVELGDTAVEFKSPSDAIKAGIVLVPESRHEEGLVVEHSVGDNLGLPQI 368

Query: 364 KALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKV 423
             L   G ++D R E  L     ++LRIK   A+  +  LSGGNQQK+++ + +A+ P V
Sbjct: 369 GQL-VRGPFIDRRREGTLTSDLIKQLRIKTPSADNKVRNLSGGNQQKIVIAKWLAIDPSV 427

Query: 424 LIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVAD 483
           +I+DEPT G+DIG+KAE+ +++  +A  G +V+VISSE AE++A SDRI+V   G +  +
Sbjct: 428 VILDEPTAGVDIGSKAEIVELIRSVASSGKSVIVISSEPAELLATSDRILVMNNGRLARE 487

Query: 484 LD 485
           ++
Sbjct: 488 IE 489



 Score = 77.0 bits (188), Expect = 2e-18
 Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 20/231 (8%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           LR VS   + G I  L G  GAG++ L +++ G      G + V  + +   SP ++ + 
Sbjct: 28  LRGVSLTIQPGTIHALVGENGAGKSTLLKILQGVVTPTEGSIEVFGEHMSSSSPENSRRL 87

Query: 335 GIMLVPEDRK-------QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387
           GI ++ +D          Q  FL+   RR         LS L   VDER E         
Sbjct: 88  GIEMIFQDLSLIPTLTVAQNIFLNREPRR---------LSIL---VDERREIAQAAEIIG 135

Query: 388 KLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSD 447
           +L +++ D  T + +LS G  Q   + +A+    ++LI+DEPT  +       +  +L  
Sbjct: 136 QLNLRV-DPRTPVFELSPGQAQLTEIAKAIHQDARILILDEPTSSLSAQEADTLFGMLKK 194

Query: 448 LADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
           L   G AV+ +S  ++E+M ++D I + R+G  V        T + ++ +M
Sbjct: 195 LTAAGTAVIYVSHRMSEIMTIADEITILRDGQNVTSGKTSEFTLDSIVQHM 245



 Score = 65.9 bits (159), Expect = 4e-15
 Identities = 57/206 (27%), Positives = 96/206 (46%), Gaps = 7/206 (3%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQ-- 86
           GE+  + G  GAG+S L ++L       AGTV      ++ + +P    + GI  + +  
Sbjct: 290 GEIVGIAGLMGAGRSELARLLFGVDKKTAGTVELGDTAVEFK-SPSDAIKAGIVLVPESR 348

Query: 87  -EFNLFPELSVAENMYLGREPR--RLGLVDWSRLRADAQALLNDLGLPL-NPDAPVRGLT 142
            E  L  E SV +N+ L +  +  R   +D  R       L+  L +   + D  VR L+
Sbjct: 349 HEEGLVVEHSVGDNLGLPQIGQLVRGPFIDRRREGTLTSDLIKQLRIKTPSADNKVRNLS 408

Query: 143 VAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGE 202
              QQ + IAK + ++  ++I+DEPTA +       +  +I  + +   SVI +S    E
Sbjct: 409 GGNQQKIVIAKWLAIDPSVVILDEPTAGVDIGSKAEIVELIRSVASSGKSVIVISSEPAE 468

Query: 203 VKAMCDRYTVMRDGRFVASGDVADVE 228
           + A  DR  VM +GR     +  ++E
Sbjct: 469 LLATSDRILVMNNGRLAREIERDEIE 494


Lambda     K      H
   0.320    0.136    0.380 

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: 658
Number of extensions: 38
Number of successful extensions: 9
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: 515
Length of database: 527
Length adjustment: 35
Effective length of query: 480
Effective length of database: 492
Effective search space:   236160
Effective search space used:   236160
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 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