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_7 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  261 bits (667), Expect = 4e-74
 Identities = 167/501 (33%), Positives = 262/501 (52%), Gaps = 15/501 (2%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L + +++K +PG  A D +DL +  GE+HALLGENGAGKSTL+KI+     AD+G V + 
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWS--RLRADA 121
           GQ +  R+ P + + LGI  ++Q F+LF  LSVA+N+ L      +G    +  +L    
Sbjct: 74  GQRVSLRN-PAQARGLGIGMVFQHFSLFETLSVAQNIALA-----MGAAAGTPKQLEPKI 127

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
           + +    G+ L P+  V  L++ E+Q VEI + +  + RL+I+DEPT+ L+ +E D L  
Sbjct: 128 REVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
            +  L A   S++++SH+LGEV+A+C   TV+R GR       A+     + RLMVG   
Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGEAA 247

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
           E      +   G   L V G++   P       L  +    R GEIVG+AG+ G G+ +L
Sbjct: 248 ELIADYPKVTGGDACLDVRGLSWHNPDPFGCS-LANIDLEVRRGEIVGIAGVAGNGQDEL 306

Query: 302 ARLIFGADPI---AAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358
             L+ G   +   A+  +    +P+    P    Q G+  VP +R   G   + S+  N 
Sbjct: 307 LALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNA 366

Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
            L + +        +       L E   ++  +K  D++     LSGGN QK +LGR + 
Sbjct: 367 LLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREIL 426

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF--- 475
             P++L+   PT G+D+GA A +H+ L  L D G A++VIS +L E+  +SDR+      
Sbjct: 427 QQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGG 486

Query: 476 REGVIVADLDAQTATEEGLMA 496
           R   + A +D + +   G MA
Sbjct: 487 RLSALHATVDTRLSDVGGWMA 507



 Score = 66.6 bits (161), Expect = 2e-15
 Identities = 60/232 (25%), Positives = 102/232 (43%), Gaps = 11/232 (4%)

Query: 18  ALDQVDLVVGVGEVHALLGENGAGKSTLIKILS--AAHAADAGTVTFAGQVLDPRDAPLR 75
           +L  +DL V  GE+  + G  G G+  L+ +LS  A    +A      G+       P  
Sbjct: 279 SLANIDLEVRRGEIVGIAGVAGNGQDELLALLSGEALLPRNASATIRFGKEPVAHLRPDA 338

Query: 76  RQQLGIATIYQE---FNLFPELSVAENMYLGREPRRL---GLVDWSRLRADAQALLNDLG 129
           R+QLG+A +  E       PELS+A+N  L      L   GL+   ++ A A+ ++   G
Sbjct: 339 RRQLGLAFVPAERLGHGAVPELSLADNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFG 398

Query: 130 LPLNPD--APVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187
           +   PD  AP R L+    Q   + + +    RL++   PT  +       +H  +  L+
Sbjct: 399 VK-TPDSQAPARSLSGGNLQKFILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALR 457

Query: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
               +++ +S  L E+  + DR   +  GR  A     D  ++D+   M G+
Sbjct: 458 DAGAAILVISEDLDELFQISDRLGALCGGRLSALHATVDTRLSDVGGWMAGQ 509



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 58/214 (27%), Positives = 97/214 (45%), Gaps = 10/214 (4%)

Query: 285 GEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRK 344
           GEI  L G  GAG++ L ++I+G     +G V+   + + LR+P  A   GI +V +   
Sbjct: 39  GEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIGMVFQ--- 95

Query: 345 QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLS 404
               F   S+ +N++L    A     Q   E   R++   Y   L     + E  +  LS
Sbjct: 96  HFSLFETLSVAQNIALAMGAAAGTPKQL--EPKIREVSRRYGMTL-----EPERLVHSLS 148

Query: 405 GGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAE 464
            G +Q+V + R +    ++LI+DEPT  +      ++   L  LA  G +++ IS +L E
Sbjct: 149 IGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFISHKLGE 208

Query: 465 VMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
           V A+     V R G +         +++ L   M
Sbjct: 209 VRALCHSATVLRGGRVAGHCVPAECSDQQLARLM 242


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: 629
Number of extensions: 35
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: 521
Length adjustment: 35
Effective length of query: 480
Effective length of database: 486
Effective search space:   233280
Effective search space used:   233280
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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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