GapMind for catabolism of small carbon sources

 

Alignments 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:

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