GapMind for catabolism of small carbon sources

 

Aligments 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_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 517

 Score =  328 bits (841), Expect = 3e-94
 Identities = 203/502 (40%), Positives = 292/502 (58%), Gaps = 13/502 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L VS + K++     L  +DL +  GEV AL GENGAGKSTL KI+        G + +
Sbjct: 9   VLSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQY 67

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            GQ   P  +  + + LGI  + QE NL P LSVAEN++L   P + G +   +LR  A 
Sbjct: 68  QGQDYRP-GSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAI 126

Query: 123 ALLNDLGLP-LNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
             +  +GL  ++PD  V  L +  QQMVEIA+ +  +  ++I+DEPTA L+ REV+ L  
Sbjct: 127 EAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
            I  L++R VS+IY+SHRL E+  +  R  V+RDG  V    +A+     +V LMVGR +
Sbjct: 187 QITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL 246

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
                   R  GA VL V G       LS    +R VSF  R GEI G++GL+GAGRT+L
Sbjct: 247 GEHIDMGARKIGAPVLTVNG-------LSRSDKVRDVSFEVRAGEIFGISGLIGAGRTEL 299

Query: 302 ARLIFGADPIAAGRVLVDD--KPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359
            RLIFGAD   +G + +    + + +RSP DA+  GI L+ EDRK +G  L  SI  N++
Sbjct: 300 LRLIFGADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIA 359

Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
           L ++  +S  G +VD   ER L +     +RI+ +     + +LSGGNQQKV++GR +  
Sbjct: 360 LGNMPGISGAG-FVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLER 418

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
              VL+ DEPTRGID+GAK +++ +L +L   G A+VV+SS+L E+M + DRI V   G 
Sbjct: 419 DCSVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGS 478

Query: 480 IVADLDAQTATEEGLMAYMATG 501
           ++   D  + T++ L+A    G
Sbjct: 479 LIDTFDRDSWTQDELLAAAFAG 500


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: 639
Number of extensions: 38
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