Alignments for a candidate for iatA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Acidovorax sp. GW101-3H11

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 Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  346 bits (887), Expect = 1e-99
 Identities = 198/499 (39%), Positives = 309/499 (61%), Gaps = 20/499 (4%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L +S + K F G+  L  V L +  GE+HAL+G+NGAGKSTLIK+L+    A  G +  
Sbjct: 18  VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGL-----VDWSRL 117
            GQ + P D+PL  Q+LGI+T+YQE NL P LSVAEN++ GR PR  G+     +DW+ L
Sbjct: 78  GGQAVWP-DSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPR-CGIAQGFRIDWATL 135

Query: 118 RADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177
              A+ L+  +GL ++    +    VA QQ+V IA+A+++ +R++I+DEPT++L   EV 
Sbjct: 136 HQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195

Query: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237
           +L  ++  L++  +S+++V+H L +V A+ DR TV+R+G +V      D+    ++  M+
Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255

Query: 238 GRHVEFERRKRRRPPG-----AVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAG 292
           GR +     +    P      A +L+ EG       L     L+ +    R GE+VGLAG
Sbjct: 256 GRDLAAASEQPAPAPAVDSRHANLLQAEG-------LGQDTQLQPLDLQIRAGEVVGLAG 308

Query: 293 LVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH 352
           L+G+GRT+LARL+FG +    G + +D + ++  +P DAI+ G+ L PE+RK  G   + 
Sbjct: 309 LLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAEL 368

Query: 353 SIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVL 412
           S+R N++L +L+A   +G+++    + +L E Y + L IK    +  IG LSGGNQQK +
Sbjct: 369 SVRENIAL-ALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAI 427

Query: 413 LGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472
           L R MA+ P++LI+DEPTRGID+ AK E+   +  LA  G+AV+ ISSE++EV+ V+ RI
Sbjct: 428 LARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRI 487

Query: 473 VVFREGVIVADLDAQTATE 491
           VV R+   V +L A ++ +
Sbjct: 488 VVLRDRRKVGELPAGSSED 506



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 75/276 (27%), Positives = 127/276 (46%), Gaps = 21/276 (7%)

Query: 241 VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
           V  +      P  A VL++ G+      ++    LR V      GEI  L G  GAG++ 
Sbjct: 3   VSMDASTAHAPAAAPVLQLSGIHKQFAGITV---LRDVQLNLYPGEIHALMGQNGAGKST 59

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           L +++ G    + G++ +  + +   SP  A + GI  V ++        + S+  N+  
Sbjct: 60  LIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRLGISTVYQE---VNLCPNLSVAENIFA 116

Query: 361 PSLKALS-ALGQWVD----ERAERDLVETYRQKLRIK--MADAETAIGKLSGGNQQKVLL 413
                   A G  +D     +  RDLV     ++ +   ++D   A+       QQ V +
Sbjct: 117 GRYPRCGIAQGFRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAV-------QQLVAI 169

Query: 414 GRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIV 473
            RA+++  +VLI+DEPT  +D     ++ +VL  L   G+++V ++  L +V AVSDRI 
Sbjct: 170 ARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRIT 229

Query: 474 VFREGVIVADLDAQTATEEGLMAYMATGTDRVAAPD 509
           V R G  V +  A+    + L+A M  G D  AA +
Sbjct: 230 VLRNGSWVGEWLAKDLGPQALIAAM-LGRDLAAASE 264


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: 655
Number of extensions: 34
Number of successful extensions: 9
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: 515
Length of database: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources