GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Rhodobacter johrii JA192

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 WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  333 bits (853), Expect = 1e-95
 Identities = 201/495 (40%), Positives = 293/495 (59%), Gaps = 15/495 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L + QVS+ F  V+ L  VD  +  GEVHAL+GENGAGKST +KIL+   A  AG V  
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 63  AGQVLDPRDAPLRRQQ--LGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120
            G+   P   P  R+    G+  I+QEFNL   L+V EN++LGRE +R   +D   ++A+
Sbjct: 65  DGR---PVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAE 121

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           ++ LL  L   ++P A V  L+V  +QMVEIAKA+ L AR++IMDEPTA L+ RE D L 
Sbjct: 122 SRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
             +  L+A   +++Y SH+L EV  + DR TV+RDGR V +     +    M   MVGR 
Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241

Query: 241 VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
           +      +  P    VL+V G+T        PG++R  SF  R GE++G AGLVG+GRT+
Sbjct: 242 LSGLFPPKSSPAPEPVLEVAGLT-------VPGFVRDASFTLRRGEVLGFAGLVGSGRTE 294

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           L   I G  P A G V ++  PL   S   A  AG++ + EDRK++G  L   +  NL+L
Sbjct: 295 LMEGIVGLRP-ATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTL 353

Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420
            +L     +   +D+ AE   +        I++ D   + G LSGGNQQK+LL + M   
Sbjct: 354 LALDRFGRV--LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411

Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480
           P+V+I+DEPTRGID+G K +++  ++ LA  G +V+V+SSEL EV+ +++R+VV   G I
Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471

Query: 481 VADLDAQTATEEGLM 495
             +++ +  TEE ++
Sbjct: 472 AGEVEGEAITEENIV 486



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 23/232 (9%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L  V F  R GE+  L G  GAG++   +++ G    +AG VL+D +P+   S R+A  A
Sbjct: 21  LFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLDGRPVHFPSSREAEAA 80

Query: 335 GIMLVPEDRK-------QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387
           G++++ ++         ++  FL   ++R             G ++D RA +   E+ R 
Sbjct: 81  GVVMIHQEFNLATPLTVEENIFLGRELKR-------------GPFLDHRAMQ--AESRRL 125

Query: 388 KLRIKMA-DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLS 446
             R+  A D    +  LS  N+Q V + +A+ L  +VLI+DEPT  +       + + + 
Sbjct: 126 LERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVD 185

Query: 447 DLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
            L   G A++  S +L EV  ++DR+ V R+G  V    A+  +E+ +   M
Sbjct: 186 RLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETM 237



 Score = 55.8 bits (133), Expect = 3e-12
 Identities = 57/218 (26%), Positives = 93/218 (42%), Gaps = 13/218 (5%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQEF 88
           GEV    G  G+G++ L++ +     A  G V   G  L P  +    +  G+  + ++ 
Sbjct: 279 GEVLGFAGLVGSGRTELMEGIVGLRPA-TGEVRMEGSPL-PHASVSAARAAGLVYLTEDR 336

Query: 89  NLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA-------LLNDLGLPLNPDAPVRG- 140
               E  +     LG     L L  + R+  D  A        ++D  + +       G 
Sbjct: 337 K---EKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGS 393

Query: 141 LTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRL 200
           L+   QQ + +AK M    R++I+DEPT  +      +++  IA L A   SVI VS  L
Sbjct: 394 LSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSEL 453

Query: 201 GEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
            EV  + +R  VM  GR     +   +   ++VRL +G
Sbjct: 454 PEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491


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: 709
Number of extensions: 33
Number of successful extensions: 9
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: 499
Length adjustment: 34
Effective length of query: 481
Effective length of database: 465
Effective search space:   223665
Effective search space used:   223665
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 24 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 (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:

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. 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:

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:

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