GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Pseudomonas simiae WCS417

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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  371 bits (952), Expect = e-107
 Identities = 209/504 (41%), Positives = 317/504 (62%), Gaps = 11/504 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL++  +SK FPGV AL  V L V  G V AL+GENGAGKSTL+KI++  +  DAG +  
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLRADA 121
            G+ +   + PL  Q+ GIA I+QE NL P +S+AEN+++GRE    L +V+   +    
Sbjct: 83  RGKPI-VFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
             LL  L + L+P+  V  L++AE+QMVEIAKA++ ++ ++IMDEPT+A++ +EV  L +
Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           IIA LK++   ++Y++H++ EV A+ D   V RDG ++       +    ++ +MVGR +
Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
                 R  P G ++L V  +T         G  + VSF    GEI+G+AGL+G+GRT++
Sbjct: 262 SQLFPLRETPIGDLLLTVRDLT-------LDGVFKDVSFDLHAGEILGIAGLMGSGRTNV 314

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           A  IFG  P ++G++ +D K +R+  P  AI+ G  L+ EDRK  G F   S+  N+ + 
Sbjct: 315 AETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 374

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
            L   +  G ++ ++A R L E   +KLR+K    E  I  LSGGNQQK LL R +   P
Sbjct: 375 VLPHYTGNG-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 433

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481
           ++LI+DEPTRGID+GAKAE++++++ LA  G+AV++ISSEL EV+ +SDR++V  EG ++
Sbjct: 434 RLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELM 493

Query: 482 ADLDAQTATEEGLMAYMATGTDRV 505
             LD   AT+E +M  +A+G   V
Sbjct: 494 GTLDRSEATQEKVM-QLASGMTAV 516


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: 604
Number of extensions: 30
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, or view the source code.

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