Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  559 bits (1440), Expect = e-164
 Identities = 299/474 (63%), Positives = 359/474 (75%), Gaps = 6/474 (1%)

Query: 34  LLGENGAGKSTLIKILSAAHAADAG--TVTFAGQVLDPRDAPLRRQQLGIATIYQEFNLF 91
           LLGENGAGKST++KIL+ A  ADAG  ++ F G VL   D P+RRQ++GI TIYQEFNL 
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 92  PELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEI 151
            ++SVAENMYLGREP R G VDW ++ +DAQ +L+DLGL + P   VR L+VAEQQMVEI
Sbjct: 61  ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120

Query: 152 AKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYT 211
           AKA+T+NA+LIIMDEPTAALSGREVD+LH II  LKA+ +S+IYVSH+L EVKA CDRYT
Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180

Query: 212 VMRDGRFVASGDVADVEVADMVRLMVGRHVEFERRKRRRPPGAVVLKVEGVTPAAP---R 268
           + RDG ++ SGDV DV V D+VRLMVGR VEF R+     PG V+LKV+ V+  A    R
Sbjct: 181 IFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGGGR 240

Query: 269 LSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLR-LRS 327
                 L  +S   R GEIVG AGLVGAGRT+LAR+IFGAD    G + V+ + +   +S
Sbjct: 241 SLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFKS 300

Query: 328 PRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387
           PR+ I AG+ LVPEDRKQQ CFL HSIR N+SLPSL  L   G ++D+RAE  L++ Y++
Sbjct: 301 PREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDYQK 360

Query: 388 KLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSD 447
           +LRIKM++   AIG LSGGNQQKV+L R MAL PKVLIVDEPTRGID+GAKAEVHQ+L D
Sbjct: 361 RLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLLFD 420

Query: 448 LADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATG 501
           +A  GVAV+VISSEL EVMAVSDRIV FREG I   + A  ATEE LMA MA G
Sbjct: 421 MARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQG 474



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 74/263 (28%), Positives = 123/263 (46%), Gaps = 24/263 (9%)

Query: 3   LLDVSQVSKSFPG----VRALDQVDLVVGV--GEVHALLGENGAGKSTLIKILSAAHAAD 56
           +L V  VS++  G    + A   +D+ V V  GE+    G  GAG++ L +++  A   D
Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284

Query: 57  AGTVTFAGQVLDPRDAPLRRQQLGIATIYQEFN---LFPELSVAENMYLGREPRRLGLVD 113
            G +   G+ + P  +P      G+A + ++      F   S+  NM L   P   GL  
Sbjct: 285 EGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSL---PSLGGLQR 341

Query: 114 WSRL---RADAQALLND----LGLPLNPDAPVRG-LTVAEQQMVEIAKAMTLNARLIIMD 165
           W      RA+ Q L+ D    L + ++ D+   G L+   QQ V +A+ M L  +++I+D
Sbjct: 342 WGMFIDDRAETQ-LIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVD 400

Query: 166 EPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRF--VASGD 223
           EPT  +       +H ++  +    V+VI +S  L EV A+ DR    R+G+   + S D
Sbjct: 401 EPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSAD 460

Query: 224 VADVEVADMVRLMVGRHVEFERR 246
            A  E+  M R+  G    F ++
Sbjct: 461 EATEELL-MARMAQGVSSSFSQQ 482


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: 742
Number of extensions: 34
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: 485
Length adjustment: 34
Effective length of query: 481
Effective length of database: 451
Effective search space:   216931
Effective search space used:   216931
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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