Alignments for a candidate for iatA in Billgrantia desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Billgrantia desiderata SP1

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_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_002151265.1:WP_086510989.1
          Length = 497

 Score =  363 bits (931), Expect = e-104
 Identities = 217/492 (44%), Positives = 302/492 (61%), Gaps = 16/492 (3%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQ--- 65
           +S  FPGVRALD V      G+VHAL+GENGAGKSTL+K+LS  +    G +   G+   
Sbjct: 11  ISMVFPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGALWIDGERHV 70

Query: 66  VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALL 125
             + R+A  +    GIA IYQE  L P ++VAEN+ LG+ P R G +   +LR  A A+L
Sbjct: 71  FANAREALAQ----GIAIIYQELTLSPNMTVAENLLLGQLPTRHGFIKRRQLRERALAIL 126

Query: 126 NDLGL-PLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIA 184
            DLG   ++P   VR L++ +QQM+EI +A+  NAR+I  DEPT++LS +E  +L  II+
Sbjct: 127 ADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLKRIIS 186

Query: 185 GLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEF 243
            L+     V+YV+HR+ EV  MCD  TV RDG+ + +   +A ++   +V  MVGR +E 
Sbjct: 187 RLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGRDIED 246

Query: 244 ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLAR 303
               R R  G V+L+++ +      L AP     VSF  R GE+ GL GLVGAGR++L R
Sbjct: 247 VYGYRERERGEVILEIDAIEGRG--LKAP-----VSFEVRRGEVFGLFGLVGAGRSELMR 299

Query: 304 LIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSL 363
           L+ GA+  +AG V    +  R  SP +AI+ GI + PEDRK QG F   S+  NL++   
Sbjct: 300 LVCGAERASAGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNISCR 359

Query: 364 KALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKV 423
           +     G   D R ER   E Y Q+L IK     TAIG LSGGNQQKV+L R +A   ++
Sbjct: 360 RFFRRWGVLRDTRRERANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLAEKIEL 419

Query: 424 LIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVAD 483
            +VDEPTRGID+GA+ +++ +L DL + G +VVVISS+LAEV ++ DRI V R+G +V  
Sbjct: 420 FVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRDGALVEV 479

Query: 484 LDAQTATEEGLM 495
           +    AT+E L+
Sbjct: 480 VPRHEATQERLL 491



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 59/242 (24%), Positives = 113/242 (46%), Gaps = 15/242 (6%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           L+ +G++   P + A   L  VSF A  G++  L G  GAG++ L +++ G +  + G +
Sbjct: 6   LRFDGISMVFPGVRA---LDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGAL 62

Query: 317 LVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDER 376
            +D +     + R+A+  GI ++ ++        + ++  NL L  L        ++  R
Sbjct: 63  WIDGERHVFANAREALAQGIAIIYQELTLSP---NMTVAENLLLGQLPTRHG---FIKRR 116

Query: 377 AERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIG 436
             R+        L        T + +LS G QQ + +GRA+    +++  DEPT  + + 
Sbjct: 117 QLRERALAILADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQ 176

Query: 437 AKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG------VIVADLDAQTAT 490
              ++ +++S L + G  V+ ++  + EV  + D + VFR+G        +A LD  T  
Sbjct: 177 ETRQLKRIISRLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLV 236

Query: 491 EE 492
            E
Sbjct: 237 SE 238


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: 649
Number of extensions: 33
Number of successful extensions: 10
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: 497
Length adjustment: 34
Effective length of query: 481
Effective length of database: 463
Effective search space:   222703
Effective search space used:   222703
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 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