GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Burkholderia phytofirmans PsJN

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 BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28215 BPHYT_RS28215 D-ribose
           transporter ATP binding protein
          Length = 509

 Score =  424 bits (1089), Expect = e-123
 Identities = 236/493 (47%), Positives = 321/493 (65%), Gaps = 10/493 (2%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L++   SKSF  VRAL   DL +  GEVHALLGENGAGKST++KIL+  H  D G +   
Sbjct: 11  LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVD 70

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLRADAQ 122
           G+       P   +  G+A IYQE  LF +LS+AEN+++GR+P  R+G + +  +R +  
Sbjct: 71  GEARRFA-TPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREVD 129

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
            LL  LG+ L  D  VRGL++A+QQ++EIAKA++LNA ++IMDEPTAALS  EV+RL  I
Sbjct: 130 GLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTI 189

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242
           +  L+ R V++++++HRL EV A+  R T+MRDG  V  G   D+    +V  MVGR +E
Sbjct: 190 VRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDLE 249

Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302
               K  RPPG V L V G+T         G  + +SF  R GEIV LAGLVGAGR+++A
Sbjct: 250 TFYPKAERPPGEVRLSVRGLTRV-------GVFKDISFDVRAGEIVALAGLVGAGRSEVA 302

Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362
           R IFG DP+ +G + +  K L    P  A++AG+ LVPEDR+QQG  L+ SI RN S+  
Sbjct: 303 RAIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTV 362

Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422
           L  L   G  +  R+E  L   +  +LR+K  D    +G LSGGNQQKV+LG+ +A  PK
Sbjct: 363 LGRLVKHG-LISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPK 421

Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482
           VLI+DEPTRGID+GAKAEV+  L++L   G+AV++ISSEL EV+ ++DR++V  EG I A
Sbjct: 422 VLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISA 481

Query: 483 DLDAQTATEEGLM 495
           D+    A EE +M
Sbjct: 482 DIARADADEERIM 494



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 68/259 (26%), Positives = 122/259 (47%), Gaps = 15/259 (5%)

Query: 263 TPAAPRLSAP------GYLRQVS---FAARGGEIVGLAGLVGAGRTDLARLIFGADPIAA 313
           T A PRL         G +R +S    A   GE+  L G  GAG++ + +++ G      
Sbjct: 5   TSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDT 64

Query: 314 GRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWV 373
           G ++VD +  R  +P +A  AG+ ++ ++      F D SI  N+ +   + +  +G+ +
Sbjct: 65  GELVVDGEARRFATPAEARDAGLAVIYQEPT---LFFDLSIAENIFM-GRQPVDRIGR-I 119

Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433
              A R  V+     L + +  A+  +  LS  +QQ + + +A++L   VLI+DEPT  +
Sbjct: 120 QYDAMRREVDGLLASLGVDLR-ADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAAL 178

Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493
            +     +  ++  L +  VA++ I+  L EV A++ R+ + R+G  V D        E 
Sbjct: 179 SLPEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEA 238

Query: 494 LMAYMATGTDRVAAPDMER 512
           ++A M         P  ER
Sbjct: 239 IVAKMVGRDLETFYPKAER 257


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: 762
Number of extensions: 47
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 509
Length adjustment: 35
Effective length of query: 480
Effective length of database: 474
Effective search space:   227520
Effective search space used:   227520
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