Alignments for a candidate for iatA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Sinorhizobium meliloti 1021

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 SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Smeli:SM_b20503
          Length = 512

 Score =  390 bits (1001), Expect = e-113
 Identities = 218/498 (43%), Positives = 319/498 (64%), Gaps = 15/498 (3%)

Query: 2   TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVT 61
           T+L++  VSK F  V+AL  VD  +  GEVHAL GENGAGKSTL+ +++       G V 
Sbjct: 5   TVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVL 64

Query: 62  FAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGR-EPRRLGLVDWSRLRAD 120
             G  +    +P   Q LGIA ++QE  L P+ ++AENM++     RR  L+++++L  D
Sbjct: 65  IEGAPVKIA-SPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERD 123

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           AQA++N L  P++    V  L ++ QQ+VEIAKA+TL+ R++I DEPTAAL+  E   L 
Sbjct: 124 AQAVMNRLA-PIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLF 182

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
            II  LKAR +S+IY+SHR+ EV ++CDR TV RDGR+VA+  V+DV   D+VRLMVGR 
Sbjct: 183 GIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGRE 242

Query: 241 VEF---ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297
           +     +++      G  +L V  +             R VSF  R GEI+G+ GL+G+G
Sbjct: 243 ISQLYPDKQPSSERLGEPILSVRDLGGER--------FRDVSFELRYGEILGVGGLIGSG 294

Query: 298 RTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN 357
           RT++A  I    P+  G + + DK LRLR   DA +AG++ + EDRK  G FLD SI +N
Sbjct: 295 RTEIAEGICALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQN 354

Query: 358 LSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAM 417
           ++   LKAL++LG  ++ R ER L E   ++L ++M   +  +  LSGGNQQKV + + +
Sbjct: 355 IAALDLKALTSLGL-LNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQL 413

Query: 418 ALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477
           A+ PKV+++DEPTRGID+GAK+E+H++L +LA  G+ ++VISSEL E++ + DR++V RE
Sbjct: 414 AVDPKVILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVRE 473

Query: 478 GVIVADLDAQTATEEGLM 495
           G I  ++     TEE +M
Sbjct: 474 GRIAGEVSGNEMTEEVIM 491



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 67/225 (29%), Positives = 109/225 (48%), Gaps = 9/225 (4%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L  V F    GE+  L G  GAG++ L  +I G    + G VL++  P+++ SP  A   
Sbjct: 22  LTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLIEGAPVKIASPAVAQSL 81

Query: 335 GIMLVPEDRKQQGCFLDHSIRRNLSLPSL-KALSALGQWVDERAERDLVETYRQKLRIKM 393
           GI LV    ++     D +I  N+ + +  +  SAL  +   + ERD         R+  
Sbjct: 82  GIALV---HQEIALCPDATIAENMFMAATNRRRSALMNYA--QLERDAQAVMN---RLAP 133

Query: 394 ADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGV 453
            D    +G L   +QQ V + +A+ L  +VLI DEPT  +       +  ++ DL   G+
Sbjct: 134 IDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFGIIRDLKARGI 193

Query: 454 AVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
           +++ IS  +AEV ++ DR+ VFR+G  VA       T + ++  M
Sbjct: 194 SIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLM 238


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: 658
Number of extensions: 32
Number of successful extensions: 8
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: 512
Length adjustment: 35
Effective length of query: 480
Effective length of database: 477
Effective search space:   228960
Effective search space used:   228960
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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
the source code
instructions for running GapMind on your computer

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