Aligments for a candidate for iatA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for iatA in Desulfovibrio vulgaris Hildenborough

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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  231 bits (588), Expect = 6e-65
 Identities = 161/498 (32%), Positives = 255/498 (51%), Gaps = 23/498 (4%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           + KSF  VRA   + L +  G + ALLGENGAGKSTL+ ILS   A D G +   G+ + 
Sbjct: 40  IGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVR 99

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128
            R +P    + GI  +YQ F L   ++VAEN+ LG+    L  V  SR+ A+  A     
Sbjct: 100 FR-SPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAARY--- 155

Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
           GL ++P A V  L++ E+Q VEI K +  ++R++I+DEPTA L+  E ++L   +  +  
Sbjct: 156 GLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAE 215

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVE-VADMVRLMVGRHVEFERRK 247
              +++++SH++ EV A+ D   ++R G  V     ++V   A++   MVGR V  E   
Sbjct: 216 NGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAA 275

Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307
               PG  VL V+G+        A   L+ +SF  R GE+  +AG+ G G+ +L   + G
Sbjct: 276 EPLEPGDRVLHVDGL--------AGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTG 327

Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367
               A G V +   P R    +   Q G+  +PEDR+     L   +  N  L + +   
Sbjct: 328 LRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLL-TARGCF 386

Query: 368 ALGQWVDER----AERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKV 423
             G ++D +    A RD++  Y     ++   AE     LSGGN QK+++GR     P +
Sbjct: 387 TRGPFLDRKSADAAARDILAEY----NVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL 442

Query: 424 LIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVAD 483
           ++ + PT+G+DI A  EV   L ++      V+++S +L EV+A++DR+ V   G  +  
Sbjct: 443 IVAENPTQGLDIAATEEVWARLLEVRS-HAGVLLVSGDLNEVLALADRVAVMYRGCFIGL 501

Query: 484 LDAQTATEEGLMAYMATG 501
           LD     +   +  M  G
Sbjct: 502 LDRSDTNKVDAIGLMMAG 519



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 64/234 (27%), Positives = 110/234 (47%), Gaps = 21/234 (8%)

Query: 285 GEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRK 344
           G I  L G  GAG++ L  ++ G      G + VD + +R RSP+DA++AGI +V     
Sbjct: 60  GRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMV----- 114

Query: 345 QQGCFLDHSIRRNLSLPSLKALSALGQWVD----ERAERDLVETYRQKLRIKMADAETAI 400
               +    +  ++++     L   G W+      R   +L   Y   +     D    +
Sbjct: 115 ----YQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAARYGLDI-----DPAARV 165

Query: 401 GKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISS 460
             LS G +Q+V + + +    +VLI+DEPT  +  G   ++ + L  +A+ G A+V IS 
Sbjct: 166 CDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIVFISH 225

Query: 461 ELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATGTD---RVAAPDME 511
           ++ EV+A++D I + R G +V +        E  +A    G +    VAA  +E
Sbjct: 226 KMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAAEPLE 279


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: 694
Number of extensions: 42
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: 524
Length adjustment: 35
Effective length of query: 480
Effective length of database: 489
Effective search space:   234720
Effective search space used:   234720
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, or view the source code.

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