Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N2E3

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 AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  373 bits (957), Expect = e-107
 Identities = 208/494 (42%), Positives = 309/494 (62%), Gaps = 10/494 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL++  VSK FPGV AL  V L V  G V AL+GENGAGKSTL+KI++  +  DAG +  
Sbjct: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-LGLVDWSRLRADA 121
            G+ +   D PL   Q GIA I+QE NL P +S+AEN+++GRE      ++D   +    
Sbjct: 87  RGKPVT-FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCT 145

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
             LL  L + L+P+  V  L++AE+QMVEIAKA++ ++ ++IMDEPT+A++ +EV  L +
Sbjct: 146 AQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           IIA LKA+   +IY++H++ EV ++ D   V RDG ++       ++   ++ +MVGR +
Sbjct: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
                 R +P G +++ V         L   G  + VSF    GEI+G+AGL+G+GRT++
Sbjct: 266 SQLFPVREKPIGDLLMSVRD-------LRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNV 318

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           A  IFG  P   G + +D +P+R+  P  AI+ G  L+ EDRK  G F   S+  N+ + 
Sbjct: 319 AEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 378

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
            L   +  G ++ ++A R L E   +KLR+K    E  I  LSGGNQQK LL R +   P
Sbjct: 379 VLPHYAGNG-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 437

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481
           ++LI+DEPTRGID+GAKAE+++++S LA  G+AV++ISSEL EV+ +SDR++V  EG ++
Sbjct: 438 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 497

Query: 482 ADLDAQTATEEGLM 495
             LD   AT+E +M
Sbjct: 498 GTLDRSEATQERVM 511



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 66/244 (27%), Positives = 122/244 (50%), Gaps = 11/244 (4%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           +L++  V+   P + A   L  V    R G ++ L G  GAG++ L ++I G     AG 
Sbjct: 27  LLEIINVSKGFPGVVA---LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGE 83

Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQWVD 374
           + +  KP+   +P  A+QAGI ++ ++       + H SI  N+ +   + L+     +D
Sbjct: 84  LRLRGKPVTFDTPLAALQAGIAMIHQELN----LMPHMSIAENIWI-GREQLNGF-HMID 137

Query: 375 ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGID 434
            R          ++LRI + D E  +G LS   +Q V + +A++    +LI+DEPT  I 
Sbjct: 138 HREMHRCTAQLLERLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAIT 196

Query: 435 IGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGL 494
               A +  +++DL   G  ++ I+ ++ EV +++D + VFR+G  +    A +   + L
Sbjct: 197 DKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSL 256

Query: 495 MAYM 498
           ++ M
Sbjct: 257 ISMM 260



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 60/223 (26%), Positives = 103/223 (46%), Gaps = 15/223 (6%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQE- 87
           GE+  + G  G+G++ + + +     +D G +   GQ +   D P    + G A + ++ 
Sbjct: 302 GEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISD-PHMAIEKGFALLTEDR 360

Query: 88  --FNLFPELSVAENMYLGREPRRLG--LVDWSRLRADAQALLNDLGLPLNPDAP-----V 138
               LFP LSV ENM +   P   G   +    LRA    L  D+   L    P     +
Sbjct: 361 KLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRA----LCEDMCKKLRVKTPSLEQCI 416

Query: 139 RGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSH 198
             L+   QQ   +A+ +  N R++I+DEPT  +       ++ +I+ L +  ++VI +S 
Sbjct: 417 DTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISS 476

Query: 199 RLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
            L EV  M DR  VM +G  + + D ++     +++L  G  V
Sbjct: 477 ELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519


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: 643
Number of extensions: 35
Number of successful extensions: 10
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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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