Alignments for a candidate for iatA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Trichormus variabilis ATCC 29413

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_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  408 bits (1048), Expect = e-118
 Identities = 230/512 (44%), Positives = 335/512 (65%), Gaps = 20/512 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L++  ++K F GV AL  V+L +  GEVHAL+GENGAGKSTL+KIL+ A+ AD G +  
Sbjct: 18  VLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRI 77

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            G+ +   D P   +Q GI  IYQE N+ P L+V EN+++G E  R   +D   +  +AQ
Sbjct: 78  NGKGVKITD-PGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRGQFLDRKAMELEAQ 136

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
            +L  LG    P   V  L +AEQQ VEIA+A+  N+R+++MDEPTAALS RE +RL  +
Sbjct: 137 QVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEV 196

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV- 241
           I  L+   +++IY+SHR+ E+ A+ DR +V+RDG+++ S    ++    +V++MVGR + 
Sbjct: 197 IRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMVGRSMQ 256

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
           +F   +R+  PG VVL+V  ++           ++  SF  R GEI+GLAGLVGAGRT++
Sbjct: 257 DFYEHQRQSNPGPVVLEVRNISDGRK-------VQPASFQLRAGEILGLAGLVGAGRTEV 309

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           +RLIFGAD   +G V ++ K L + SP DAI  GI  VPEDRK QG FL+ S R+N+ L 
Sbjct: 310 SRLIFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKNIGLN 369

Query: 362 SLKALSALG--QWVD-ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
            LK  + LG   W    +   D VE +     I++A+ E     LSGGNQQK+LL R +A
Sbjct: 370 RLKQDANLGIVNWGSVNKIATDAVENF----HIRLANLEIRAVDLSGGNQQKLLLARWLA 425

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478
           + P+VL++DEPTRG+DIGAK+E+++++SDL+  GVA++++SSEL E++ +SDR++V REG
Sbjct: 426 INPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREG 485

Query: 479 VIVADLD---AQTATEEGLMAYMATGTDRVAA 507
            +V +LD    +  T+E +M Y ATG   V A
Sbjct: 486 QLVGELDNSIGKEITQENIMHY-ATGASEVTA 516



 Score = 88.2 bits (217), Expect = 7e-22
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 18/253 (7%)

Query: 251 PPGAV--VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGA 308
           PP     VL+++G+   A R      L+ V+     GE+  L G  GAG++ L +++ GA
Sbjct: 11  PPATATPVLEMQGI---AKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGA 67

Query: 309 DPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS---LKA 365
                G + ++ K +++  P  A QAGI L+         + + ++  NL++     + +
Sbjct: 68  YIADEGEIRINGKGVKITDPGTARQAGINLI---------YQELNVAPNLTVTENIFMGS 118

Query: 366 LSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLI 425
               GQ++D +A     +     L    A  +  +G L+   QQ+V + RA+    ++L+
Sbjct: 119 ELTRGQFLDRKAMELEAQQVLASLGASFAPTD-IVGTLAIAEQQQVEIARALKDNSRILV 177

Query: 426 VDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLD 485
           +DEPT  +       + +V+  L + G+A++ IS  + E+ A++DRI V R+G  +  L 
Sbjct: 178 MDEPTAALSDRETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLT 237

Query: 486 AQTATEEGLMAYM 498
            +  + + L+  M
Sbjct: 238 REEISPQRLVQMM 250


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: 654
Number of extensions: 30
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 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:

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 2024 update 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