Alignments for a candidate for iatA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  386 bits (991), Expect = e-111
 Identities = 219/488 (44%), Positives = 312/488 (63%), Gaps = 9/488 (1%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           + K+FPGV+ALD +  V   G+VHAL+GENGAGKSTL+KIL  A+   +G +    + +D
Sbjct: 21  IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128
            +         G+A I+QE +L PE++VAEN++LG  P   GL++ S LR  A A L  L
Sbjct: 81  FKSTADSIGS-GVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGL 139

Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
              ++P   V  L++ ++Q+VEIAKA++  A +I  DEPT++LS RE+DRL AII  L+ 
Sbjct: 140 ADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRD 199

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247
               V+YVSHR+ EV  +C+  TV +DGR+V +  D++ +    +V  MVGR ++     
Sbjct: 200 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQDIYDY 259

Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307
           R R  GAV LKV+G       L  PG    VSF    GEI+GL GLVGAGRT+L RL+ G
Sbjct: 260 RPRQRGAVALKVDG-------LLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSG 312

Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367
               +AG++ +    L+LRSPRDAI AGI+L PEDRK++G     S+  N+++ +  A S
Sbjct: 313 LARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHS 372

Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427
             G  +    E+D  E   + L++K  +A   I  LSGGNQQK +LGR +++  KVL++D
Sbjct: 373 TFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432

Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487
           EPTRGIDIGAKAE++Q++ +LA  G+AV+V+SS+L EVM +SDRI+V  EG +  +L  +
Sbjct: 433 EPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSRE 492

Query: 488 TATEEGLM 495
            A E  L+
Sbjct: 493 QANESNLL 500



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 63/258 (24%), Positives = 110/258 (42%), Gaps = 32/258 (12%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           L+  G+    P + A   L  +SF A  G++  L G  GAG++ L +++ GA    +G +
Sbjct: 16  LRFNGIGKTFPGVKA---LDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGAL 72

Query: 317 LVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRR----NLSLPSLKA 365
            + ++ +  +S  D+I +G+        LVPE    +  FL H        N S    +A
Sbjct: 73  QIGERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQA 132

Query: 366 LSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLI 425
           L+ L    DE                   D +  +G+LS G +Q V + +A++    V+ 
Sbjct: 133 LACLKGLADE------------------IDPQEKVGRLSLGQRQLVEIAKALSRGAHVIA 174

Query: 426 VDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLD 485
            DEPT  +       +  ++  L D G  V+ +S  + EV  + + + VF++G  V   D
Sbjct: 175 FDEPTSSLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFD 234

Query: 486 AQTATEEGLMAYMATGTD 503
             +      +     G D
Sbjct: 235 DMSQLTHDQLVTCMVGRD 252


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: 690
Number of extensions: 30
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: 514
Length adjustment: 35
Effective length of query: 480
Effective length of database: 479
Effective search space:   229920
Effective search space used:   229920
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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