GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

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 HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  383 bits (984), Expect = e-111
 Identities = 215/511 (42%), Positives = 326/511 (63%), Gaps = 18/511 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           ++ +  V K FPGV ALD     +  GEVHAL+GENGAGKSTL+KILS  +  D+G +  
Sbjct: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR-LGL-VDWSRLRAD 120
            G+ ++  + P + Q LGI  I+QE NL   LS A+N+++GREPR+ +GL +D   L   
Sbjct: 82  DGKPVEITE-PRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           A A+   + L ++P  PV  LTVA QQMVEIAKA++ ++R++IMDEPTAAL+  E+  L 
Sbjct: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
            II  L+A+ V ++Y+SH++ E++ + DR +VMRDG+++A+  + +  +  ++ +MVGR 
Sbjct: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260

Query: 241 VEFERRKRRRPPGA----VVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGA 296
           ++ E   +R PP      VVL+V G       L+    +R VSF  R GEI+G AGL+GA
Sbjct: 261 LDGE---QRIPPDTSRNDVVLEVRG-------LNRGRAIRDVSFTLRKGEILGFAGLMGA 310

Query: 297 GRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356
           GRT++AR IFGADP+ AG +++      ++SP DA+  GI  + EDRK  G  +   ++ 
Sbjct: 311 GRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370

Query: 357 NLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRA 416
           N++L S+   + +G ++D+RA R+  + Y ++L IK    E     LSGGNQQK+++ + 
Sbjct: 371 NIALSSMGRFTRVG-FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKW 429

Query: 417 MALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFR 476
           +     +L  DEPTRGID+GAK+E++++L  LA+ G A+V+ISSEL EV+ +S R++V  
Sbjct: 430 LLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMC 489

Query: 477 EGVIVADLDAQTATEEGLMAYMATGTDRVAA 507
           EG I  +L    AT+E +M         VA+
Sbjct: 490 EGRITGELARADATQEKIMQLATQRESAVAS 520


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: 654
Number of extensions: 34
Number of successful extensions: 9
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: 520
Length adjustment: 35
Effective length of query: 480
Effective length of database: 485
Effective search space:   232800
Effective search space used:   232800
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.

Links

Downloads

Related tools

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