GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  388 bits (997), Expect = e-112
 Identities = 223/496 (44%), Positives = 322/496 (64%), Gaps = 7/496 (1%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD-AGTVTF 62
           L++  +S++FPGV+ALD+V+L +  GEV AL GENGAGKSTL+KIL+  +A D  GT+  
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121
            GQ +   D+   R  LG+  IYQE  +   L+V EN++L REPR RLGL+D  R+  +A
Sbjct: 70  EGQEVALADSHHART-LGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREA 128

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
           + +L  + + ++P   V  L+V +QQM+EIAKA+   ++ IIMDEPTA+LS  E   L  
Sbjct: 129 REVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLG 188

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           I+  L+ R+++V+Y+SHRL E+  + DR TV+RDGR V +  +AD+    +VRLMV R +
Sbjct: 189 IVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAREL 248

Query: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
            E     +       VL+V  ++    R + P  +R +SF    GE++G+AGLVG+GRT+
Sbjct: 249 SELYGEPQSHASRDPVLEVRALSLKPVRKAEPR-IRDISFTLHRGEVLGIAGLVGSGRTE 307

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           +  +IFG      G V ++ KP+ +R+P DAI++GI  V EDRK QG  L  ++R N SL
Sbjct: 308 IMEMIFGMRA-CTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSL 366

Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420
             L+  S   Q+V    ER+    + + L IK    E  +  LSGGNQQK+++ + +A +
Sbjct: 367 THLERYSPF-QFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARS 425

Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480
           PKVLIVDEPTRGID+GAKAEVH +++ LA  G+ V+VISS+L EV+AVSDRI+  REG I
Sbjct: 426 PKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRI 485

Query: 481 VADLDAQTATEEGLMA 496
             +L    A++E +MA
Sbjct: 486 SGELSRAQASQEKVMA 501



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 65/254 (25%), Positives = 114/254 (44%), Gaps = 24/254 (9%)

Query: 253 GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGA-DPI 311
           G   L++  ++   P + A   L +V+   R GE++ LAG  GAG++ L +++ G   P 
Sbjct: 6   GVPFLEMRNISRTFPGVKA---LDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPD 62

Query: 312 AAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQG-------CFLDHSIRRNLSLPSLK 364
             G +LV+ + + L     A   G+ ++ ++    G        FL    R  L L    
Sbjct: 63  PGGTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRP 122

Query: 365 ALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVL 424
            +         R  R+++ T    +     D  T + +LS G QQ + + +A+    K +
Sbjct: 123 RMY--------REAREVLATIDMDI-----DPATRVSELSVGQQQMIEIAKALCARSKAI 169

Query: 425 IVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL 484
           I+DEPT  +     + +  ++  L +  +AVV IS  L E+  ++DR+ V R+G  V   
Sbjct: 170 IMDEPTASLSHHETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTA 229

Query: 485 DAQTATEEGLMAYM 498
                T E L+  M
Sbjct: 230 PIADMTRETLVRLM 243


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: 672
Number of extensions: 35
Number of successful extensions: 9
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: 505
Length adjustment: 34
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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 (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