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

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:

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, 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

GapMind for catabolism of small carbon sources