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_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  380 bits (977), Expect = e-110
 Identities = 218/497 (43%), Positives = 319/497 (64%), Gaps = 16/497 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L +  VSK FPGV ALD +DL +  GEVHA+ GENGAGKSTL+KI+S  + AD G V +
Sbjct: 23  ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRY 82

Query: 63  AG---QVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119
            G   Q     DA    Q  GIA I+QE NL P LSVAEN+YL REP+R   VD+  L +
Sbjct: 83  RGAPVQFSSTSDA----QAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNS 138

Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179
           +AQ  L  +GL ++P   V  L++A+QQMVEIAKA++L+AR++IMDEPT++L+  E  +L
Sbjct: 139 NAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQL 198

Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
             II  L+A  V+++Y+SHRL E+  + DR TV+RDGR +A+ D A   V ++V  MVGR
Sbjct: 199 FRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGR 258

Query: 240 HVEFERRKRR-RPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298
            ++     R+  P   ++L+V         L   G    +SF  R GEI+G AGL+GAGR
Sbjct: 259 PLDDAYPPRQSTPSNQILLRVRD-------LQRTGVFGPLSFELRKGEILGFAGLMGAGR 311

Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358
           T+ AR IFGA+   +G + + D+P+ + SPR+AI+ GI  + EDRK+ G  L   +  N+
Sbjct: 312 TETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANI 371

Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
           +L +++A+S+ G ++    E  + E Y ++L I+    +     LSGGNQQK+++ + + 
Sbjct: 372 TLANVRAISSRG-FLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLY 430

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478
              ++L  DEPTRGID+GAK  ++ ++  LA  GV VV+ISSEL E++ ++DRI VF EG
Sbjct: 431 RGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEG 490

Query: 479 VIVADLDAQTATEEGLM 495
            I A L+ +  ++E ++
Sbjct: 491 RITAVLETRQTSQEEIL 507



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 68/249 (27%), Positives = 122/249 (48%), Gaps = 12/249 (4%)

Query: 251 PPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADP 310
           P    +L+++GV+   P + A   L  +      GE+  + G  GAG++ L ++I G   
Sbjct: 18  PVSREILQLKGVSKRFPGVVA---LDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYR 74

Query: 311 IAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSAL 369
              G V     P++  S  DA  AGI ++ ++       + H S+  N+ L         
Sbjct: 75  ADEGVVRYRGAPVQFSSTSDAQAAGIAIIHQELN----LVPHLSVAENIYLAREPKR--- 127

Query: 370 GQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEP 429
           G +VD R      +   Q++ + ++ + T +G LS   QQ V + +A++L  +VLI+DEP
Sbjct: 128 GPFVDYRTLNSNAQRCLQRIGLNVSPS-TLVGALSLAQQQMVEIAKALSLDARVLIMDEP 186

Query: 430 TRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTA 489
           T  +      ++ +++ +L   GVA++ IS  L E+  + DR+ V R+G  +A  D  + 
Sbjct: 187 TSSLTESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFAST 246

Query: 490 TEEGLMAYM 498
           T   ++A M
Sbjct: 247 TVNEIVARM 255



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 52/217 (23%), Positives = 98/217 (45%), Gaps = 7/217 (3%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVL---DPRDAPLRRQQLGIATIY 85
           GE+    G  GAG++   + +  A   D+G++T   + +    PR+A +R     ++   
Sbjct: 298 GEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREA-IRHGIAYLSEDR 356

Query: 86  QEFNLFPELSVAENMYLG--REPRRLGLVDWSRLRADAQALLNDLGLPLNPDAPV-RGLT 142
           ++  L   + V+ N+ L   R     G + +S   A A+  + +LG+       + R L+
Sbjct: 357 KKDGLALSMPVSANITLANVRAISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLS 416

Query: 143 VAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGE 202
              QQ + I+K +   +R++  DEPT  +       ++ ++  L A  V V+ +S  L E
Sbjct: 417 GGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPE 476

Query: 203 VKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
           +  M DR  V  +GR  A  +       +++    GR
Sbjct: 477 LLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASGR 513


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: 640
Number of extensions: 29
Number of successful extensions: 8
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: 516
Length adjustment: 35
Effective length of query: 480
Effective length of database: 481
Effective search space:   230880
Effective search space used:   230880
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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