Alignments for a candidate for iatA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Pseudomonas simiae WCS417

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 GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__WCS417:GFF4164
          Length = 499

 Score =  384 bits (987), Expect = e-111
 Identities = 218/488 (44%), Positives = 310/488 (63%), Gaps = 9/488 (1%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           + K FPGV+AL Q+       EVHAL+GENGAGKSTL+KIL  A+   +GT+    Q +D
Sbjct: 11  IGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQIGEQTMD 70

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128
            + A       G+A I+QE +L PE++VAEN++LG  P R G+V+ S+LR  A A L  L
Sbjct: 71  FKSAA-DSIACGVAVIHQELHLVPEMTVAENLFLGHLPTRFGVVNRSQLRKQALACLKGL 129

Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
              ++PD  +  L++ ++Q+VEIAKA++  A +I  DEPT++LS RE+DRL AII  L+ 
Sbjct: 130 ADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIITRLRD 189

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD-MVRLMVGRHVEFERRK 247
               V+YVSHR+ EV  +C+  TV +DGR+V + D  +    D +V  MVGR ++     
Sbjct: 190 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMNALSHDQLVTCMVGRDIQDIYDY 249

Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307
           R+R  G V LKVEG       L  PG    VS     GEI+GL GLVGAGRT+L RL+ G
Sbjct: 250 RQREQGEVALKVEG-------LLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLLSG 302

Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367
                AG + +  + L+LRSPRDAI AG++L PEDRK++G     S+  N+++ +  A S
Sbjct: 303 LTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHS 362

Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427
             G  + +  E    +   + +++K  +AE  I  LSGGNQQK +LGR +++  KVL++D
Sbjct: 363 TFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 422

Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487
           EPTRGIDIGAK+E++Q++ +LA  G+AV+V+SS+L EVM +SDRI+V  EG +  +L   
Sbjct: 423 EPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTRD 482

Query: 488 TATEEGLM 495
            A E  L+
Sbjct: 483 QADEARLL 490



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 67/258 (25%), Positives = 113/258 (43%), Gaps = 32/258 (12%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           L+  G+    P + A   L Q+SF AR  E+  L G  GAG++ L +++ GA   ++G +
Sbjct: 6   LRFNGIGKEFPGVKA---LSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTL 62

Query: 317 LVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRR----NLSLPSLKA 365
            + ++ +  +S  D+I  G+        LVPE    +  FL H   R    N S    +A
Sbjct: 63  QIGEQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLPTRFGVVNRSQLRKQA 122

Query: 366 LSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLI 425
           L+ L    DE                   D +  +G+LS G +Q V + +A++    V+ 
Sbjct: 123 LACLKGLADE------------------IDPDEKLGRLSLGQRQLVEIAKALSRGAHVIA 164

Query: 426 VDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLD 485
            DEPT  +       +  +++ L D G  V+ +S  + EV  + + + VF++G  V   D
Sbjct: 165 FDEPTSSLSAREIDRLMAIITRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFD 224

Query: 486 AQTATEEGLMAYMATGTD 503
              A     +     G D
Sbjct: 225 DMNALSHDQLVTCMVGRD 242



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 65/234 (27%), Positives = 107/234 (45%), Gaps = 12/234 (5%)

Query: 14  PGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD---PR 70
           PG+R  + V L V  GE+  L G  GAG++ L ++LS    + AG++   GQ L    PR
Sbjct: 267 PGLR--EPVSLNVHKGEILGLFGLVGAGRTELFRLLSGLTRSTAGSLALCGQTLQLRSPR 324

Query: 71  DAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-----LGLVDWSRLRADAQALL 125
           DA +    L      ++  + P  SVAEN+ +           L    W    AD Q   
Sbjct: 325 DA-IAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLRDGWETTNADRQIKA 383

Query: 126 NDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAG 185
             +  P N +  +  L+   QQ   + + +++  +++++DEPT  +       ++ II  
Sbjct: 384 MKVKTP-NAEQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKSEIYQIIHN 442

Query: 186 LKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
           L A  ++VI VS  L EV  + DR  VM +G           + A +++L + R
Sbjct: 443 LAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTRDQADEARLLQLALPR 496


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: 650
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: 499
Length adjustment: 34
Effective length of query: 481
Effective length of database: 465
Effective search space:   223665
Effective search space used:   223665
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)
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Protein sequences (fasta format)
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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