Alignments for a candidate for iatA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments 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_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  389 bits (998), Expect = e-112
 Identities = 221/496 (44%), Positives = 319/496 (64%), Gaps = 11/496 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           L+ V ++SK FPGVRAL +V   +  GEVHAL+GENGAGKSTL+KIL+  +  D G + +
Sbjct: 4   LISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILY 63

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGL-VDWSRLRAD 120
            GQ +D + +P   Q +G+  I+QE  L   L++A+NM++GREPR RLGL +D  +L A 
Sbjct: 64  EGQPVDFQ-SPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQ 122

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           A  +L  + + L+P A V  LTVA QQMVEIAKA++ ++R++IMDEPT+AL+  E+  L 
Sbjct: 123 AHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELF 182

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
            II  LK R V +IY+SH++ E+K + DR TV+RDG +VA+  V D  V  ++ +MVGR 
Sbjct: 183 RIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRT 242

Query: 241 V-EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299
           + +    +     G V L+V        RL+A   +R VSFA R GEI+G AGL+GAGRT
Sbjct: 243 LTDAAPSQHIANQGEVALEVT-------RLNAGPLVRDVSFALRKGEILGFAGLMGAGRT 295

Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359
           ++AR +FGADPI +G ++V      +R+P DA+  GI  + EDRK+ G     S+  N+ 
Sbjct: 296 EVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIV 355

Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
           + +L+   +L  ++     R     +   L I+   A   +  LSGGNQQK+++ + +  
Sbjct: 356 MSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLER 415

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
              VL  DEPTRGID+GAK+E++++L  LAD G A+V+ISSEL E++ +SDRIVV  EG 
Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGR 475

Query: 480 IVADLDAQTATEEGLM 495
           I  +L A  AT+E +M
Sbjct: 476 ITGELAAAGATQERIM 491



 Score = 99.4 bits (246), Expect = 3e-25
 Identities = 62/235 (26%), Positives = 122/235 (51%), Gaps = 7/235 (2%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L +V F    GE+  L G  GAG++ L +++ G      G +L + +P+  +SPR+A   
Sbjct: 20  LHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILYEGQPVDFQSPREAQAV 79

Query: 335 GIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKM 393
           G+ ++ ++ +     ++H +I +N+ +   +    LG ++DE            ++ + +
Sbjct: 80  GVGIIHQELQ----LMNHLTIAQNMFI-GREPRGRLGLFLDEDKLNAQAHDILARMHVTL 134

Query: 394 ADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGV 453
            D    +  L+   QQ V + +A++   +VLI+DEPT  ++    AE+ +++ DL   GV
Sbjct: 135 -DPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRDLKKRGV 193

Query: 454 AVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATGTDRVAAP 508
            ++ IS ++ E+  ++DR+ V R+G  VA +  +  T + ++  M   T   AAP
Sbjct: 194 GIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRTLTDAAP 248


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: 639
Number of extensions: 35
Number of successful extensions: 8
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: 503
Length adjustment: 34
Effective length of query: 481
Effective length of database: 469
Effective search space:   225589
Effective search space used:   225589
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
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