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_523 Inositol transport system ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  377 bits (968), Expect = e-109
 Identities = 214/494 (43%), Positives = 310/494 (62%), Gaps = 10/494 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL+V  VSK FPGV AL  V L V  G V AL+GENGAGKSTL+KI++  +  DAG +  
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-LGLVDWSRLRADA 121
            G+ +   D PL   Q GIA I+QE NL P +S+AEN+++GRE    L +VD   +    
Sbjct: 86  RGKPVT-FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCT 144

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
             LL  L + L+P+  V  L++AE+QMVEIAKA++ ++ ++IMDEPT+A++  EV  L +
Sbjct: 145 ARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFS 204

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           IIA LK++   +IY++H++ EV A+ D   V RDG ++       ++   ++ +MVGR +
Sbjct: 205 IIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 264

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
                 R +P G +VL V         LS  G  + VSF    GEI+G+AGL+G+GRT++
Sbjct: 265 SQLFPVREQPIGDLVLSVRD-------LSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNV 317

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           A  IFG  P   G +L+D +P+R+  P  AI+ G  L+ EDRK  G F   S+  N+ + 
Sbjct: 318 AEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 377

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
            L      G ++ ++A R L E   +KLR+K    E  I  LSGGNQQK LL R +   P
Sbjct: 378 VLPHYVGNG-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 436

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481
           ++LI+DEPTRGID+GAKAE+++++S LA  G+AV++ISSEL EV+ +SDR++V  EG ++
Sbjct: 437 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 496

Query: 482 ADLDAQTATEEGLM 495
             L+   AT+E +M
Sbjct: 497 GTLNRGEATQERVM 510



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 71/249 (28%), Positives = 124/249 (49%), Gaps = 11/249 (4%)

Query: 251 PPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADP 310
           P    +L+V  V+   P + A   L  V    R G ++ L G  GAG++ L ++I G   
Sbjct: 21  PDEPYLLEVVNVSKGFPGVVA---LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQ 77

Query: 311 IAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSAL 369
             AG + +  KP+   +P  A+QAGI ++ ++       + H SI  N+ +   + L+ L
Sbjct: 78  PDAGELRLRGKPVTFDTPLAALQAGIAMIHQELN----LMPHMSIAENIWI-GREQLNGL 132

Query: 370 GQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEP 429
              VD            ++LRIK+ D E  +G LS   +Q V + +A++    +LI+DEP
Sbjct: 133 -HMVDHGEMHRCTARLLERLRIKL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEP 190

Query: 430 TRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTA 489
           T  I     A +  +++DL   G  ++ I+ ++ EV A++D + VFR+G  +    A + 
Sbjct: 191 TSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSM 250

Query: 490 TEEGLMAYM 498
             + L++ M
Sbjct: 251 DGDSLISMM 259


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: 660
Number of extensions: 38
Number of successful extensions: 10
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: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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)
Organisms (tab-delimited)
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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