GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Desulfovibrio vulgaris Miyazaki F

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 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__Miya:8502321 DvMF_3029 ABC transporter related
           (RefSeq)
          Length = 537

 Score =  228 bits (581), Expect = 4e-64
 Identities = 162/497 (32%), Positives = 249/497 (50%), Gaps = 20/497 (4%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQ--- 65
           + KSF  VRA   + L +  G + ALLGENGAGKSTL+ IL+     DAGT+   G    
Sbjct: 35  ICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTV 94

Query: 66  VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALL 125
              PRDA     + GI  +YQ F L   ++VAEN+ LG+ P  L  +  +R+R +  AL 
Sbjct: 95  FASPRDA----LRAGIGMVYQHFMLVDSMTVAENVLLGQSPDML--LRPARMRDEVAALA 148

Query: 126 NDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAG 185
              GL ++P A V GL++ E+Q VEI K +  ++R++I+DEPTA L+ RE D+L   +  
Sbjct: 149 ERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMWR 208

Query: 186 LKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADV-EVADMVRLMVGRHVEFE 244
           +  +  +++++SH+L EV  + D   ++R G  V     ADV     +   MVGR V  +
Sbjct: 209 MADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDVVLQ 268

Query: 245 RRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARL 304
              +R  P   VL VE ++ A         L  VS   R GEIV +AG+ G G+ +L   
Sbjct: 269 VDAKRLTPVDTVLSVEHLSGAG--------LSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320

Query: 305 IFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLK 364
           I G     AG V +  +P R        + G+  +PEDR+         +  N  L +  
Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRN 380

Query: 365 ALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVL 424
              A G ++D     + V+    +  ++  D       LSGGN QK+++GR     P+V+
Sbjct: 381 QF-AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVI 439

Query: 425 IVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL 484
           + + PT+G+DI A  EV   L +       V++++ +L E + ++DRI V   G  +   
Sbjct: 440 VAENPTQGLDISATEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVF 498

Query: 485 DAQTATEEGLMAYMATG 501
           D     +   +  M  G
Sbjct: 499 DKDDTAKVQAIGLMMAG 515



 Score = 89.4 bits (220), Expect = 3e-22
 Identities = 77/261 (29%), Positives = 127/261 (48%), Gaps = 16/261 (6%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           V++++G+  +  ++ A      ++   R G I  L G  GAG++ L  ++ G     AG 
Sbjct: 29  VVRLDGICKSFGKVRAN---HDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGT 85

Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSL-PSLKALSALGQWV 373
           ++VD  P    SPRDA++AGI +V     Q    +D  ++  N+ L  S   L    +  
Sbjct: 86  IVVDGVPTVFASPRDALRAGIGMV----YQHFMLVDSMTVAENVLLGQSPDMLLRPARMR 141

Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433
           DE A   L E Y   +     D    +G LS G +Q+V + + +    +VLI+DEPT  +
Sbjct: 142 DEVAA--LAERYGLAV-----DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVL 194

Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493
                 ++ + +  +AD G A+V IS +L EV+ V+D I + R G +V +        + 
Sbjct: 195 TPRETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQT 254

Query: 494 LMAYMATGTDRVAAPDMERLT 514
           ++A    G D V   D +RLT
Sbjct: 255 VLANRMVGRDVVLQVDAKRLT 275


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: 700
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: 537
Length adjustment: 35
Effective length of query: 480
Effective length of database: 502
Effective search space:   240960
Effective search space used:   240960
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 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