Alignments for a candidate for iatA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Klebsiella michiganensis M5al

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 BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  374 bits (959), Expect = e-108
 Identities = 210/494 (42%), Positives = 307/494 (62%), Gaps = 10/494 (2%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L+   +SK FPGV+ALD V L V  G VHAL+GENGAGKSTL+K L   +  D G +   
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA 123
           G+ +  +D  +   + GI+ I+QE NL P ++VAEN++LGREP + G VD  +L    Q 
Sbjct: 66  GEPVQFQDT-MDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQD 124

Query: 124 LLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAII 183
           LL+ L + L+ D  V  L++A QQMVEIAKA++ NA ++IMDEPT+AL+  EV  L  II
Sbjct: 125 LLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTII 184

Query: 184 AGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEF 243
             L+ +  ++IY+SH++ E+ A+ D  +V RDG +V S    +     ++  MVGR +  
Sbjct: 185 RDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELTQ 244

Query: 244 ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLAR 303
              K     G  VL V         LS  G    ++F+ R GEI+G+AGLVGAGR+++  
Sbjct: 245 LFPKFNNAIGEEVLTVR-------NLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVME 297

Query: 304 LIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSL 363
            +FG +   +G VL+D  P+ + SP  AI+ G+ L+ EDRK+ G FL  S+  N+S+  +
Sbjct: 298 SLFGMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKM 357

Query: 364 KALSALGQWVDE-RAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422
                   +V   +   D +E  R +L IK    +  I  LSGGNQQKVL+ R +   PK
Sbjct: 358 PEYIGKTGFVQHLKMAEDCMEQIR-RLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPK 416

Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482
           +LI+DEPTRGID+GAKAE++ ++S+LA+ GVAV+++SSEL E++ +SDR++V  EG I  
Sbjct: 417 ILILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITG 476

Query: 483 DLDAQTATEEGLMA 496
            LD + A +E +++
Sbjct: 477 ILDKEDADQETILS 490



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 66/246 (26%), Positives = 121/246 (49%), Gaps = 12/246 (4%)

Query: 254 AVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAA 313
           A  L+ EG++   P + A   L  VS   R G +  L G  GAG++ L + + G      
Sbjct: 3   AFALEAEGISKFFPGVKA---LDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDK 59

Query: 314 GRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQW 372
           G + V  +P++ +   DA+++GI ++ ++       + H ++  N+ L           +
Sbjct: 60  GAIRVKGEPVQFQDTMDALRSGISMIHQELN----LVPHMTVAENIWLGREPMKYG---F 112

Query: 373 VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432
           VD R      +    KL I+++ A+  +G+LS  +QQ V + +A++    ++I+DEPT  
Sbjct: 113 VDHRQLARQTQDLLDKLNIRLS-ADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSA 171

Query: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEE 492
           +     A +  ++ DL   G A++ IS ++ E+ A++D I VFR+G  V        T +
Sbjct: 172 LTESEVAHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQ 231

Query: 493 GLMAYM 498
            L+  M
Sbjct: 232 SLITQM 237



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 64/225 (28%), Positives = 107/225 (47%), Gaps = 8/225 (3%)

Query: 18  ALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQ 77
           A   ++  V  GE+  + G  GAG+S +++ L     AD+G V   G  ++  D+P    
Sbjct: 268 AFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEVLIDGMPVNI-DSPSTAI 326

Query: 78  QLGIATIYQE---FNLFPELSVAENMYLGREPR---RLGLVDWSRLRADAQALLNDLGLP 131
           + G+A + ++     LF  LSV ENM + + P    + G V   ++  D    +  L + 
Sbjct: 327 EKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIK 386

Query: 132 L-NPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARS 190
               D  +  L+   QQ V IA+ +    +++I+DEPT  +       ++ +I+ L  R 
Sbjct: 387 TPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDVGAKAEIYHLISELANRG 446

Query: 191 VSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235
           V+VI VS  L E+  M DR  VM +GR     D  D +   ++ L
Sbjct: 447 VAVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDADQETILSL 491


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: 609
Number of extensions: 36
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: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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