GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Sinorhizobium meliloti 1021

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate SMc02437 SMc02437 phosphoenolpyruvate phosphotransferase PTSP (enzyme I-Ntr) protein

Query= reanno::WCS417:GFF4500
         (838 letters)



>FitnessBrowser__Smeli:SMc02437
          Length = 755

 Score =  235 bits (599), Expect = 8e-66
 Identities = 180/613 (29%), Positives = 294/613 (47%), Gaps = 23/613 (3%)

Query: 234 EDAEAAIKALVALLAE--GCGEAVVNVAEP--VATQSSATLLRGVCASPGSAFGQVVQVT 289
           ED   A++    +LAE    GE +  + +P      S    + G     G   G VV + 
Sbjct: 143 EDEVEALETTAMVLAEMVATGE-LKKITKPGLELDLSRPVTIEGNSYGEGIGLGYVV-LH 200

Query: 290 DPELVITE---QGTGGATERAALTRGLLAAN-EALQVLQDKAAGSAQAEIFRAHQELLED 345
           +P +V+T    + T    +R A   G L  + + +   +D +       +   ++    D
Sbjct: 201 EPRIVVTNLLNEDTEHELQRLAEALGSLRISIDDMLSRRDVSMEGEHRAVLETYRMFAHD 260

Query: 346 PTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI-- 403
              +      +  G +A  A       T      L +  + ER  D  D+  R+L+ +  
Sbjct: 261 RGWVRKLEEAIRNGLTAEAAVERVQSETKARMIRLTDPYLRERMHDFDDLANRLLRQLSG 320

Query: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463
            G + SA D P  AI++A  +  ++        V G V   G  TSHV I+ARA+G+P +
Sbjct: 321 YGAKLSAADFPNDAIVVARAMGAAELLDYPRENVRGLVLEEGAVTSHVVIVARAMGIPVV 380

Query: 464 CGVPAQVLALA-NGKQVLLDADKGELHLEPNLAEIEQ-LEAARKHQVLRHQRDVAQASLP 521
            G  A  +ALA N   +++D D  ++HL P +A++++  E   + +  R  +  A   + 
Sbjct: 381 -GQAAGAVALAENRDAIIVDGDDAKVHLRP-MADLQRAYEEKVRFRARRQAQFRALRDVE 438

Query: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581
             T+DG  + +  N   L ++ H    G EG+GL R+E  ++  +  P  EEQ   Y  +
Sbjct: 439 PLTKDGKRITLQMNAGLLVDLPHLNEAGAEGIGLFRTELQFMIASTMPKAEEQEAFYRNV 498

Query: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641
            +     + +  RTLD+GGDK + Y     E NP LG R IRL L+RP LLR QFRA+L 
Sbjct: 499 MKQT-AGKPVTFRTLDIGGDKVVPYFRAAEEENPALGWRAIRLSLDRPGLLRTQFRAMLR 557

Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEE-----ALALGLTELPKLGIMIEVPSAALMA 696
           +   A L +MLPMV+ ++EL  AR++L++E      L   L    + G M+EVP+     
Sbjct: 558 ATAGAELKMMLPMVTEVAELKSARELLQKEIERQSKLGEQLPRKLQFGAMLEVPALLWQL 617

Query: 697 DVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWV 756
           D     VDF S+G+NDL Q+ +A+DR + R++ + D      LR++   V+A   +   V
Sbjct: 618 DELMAEVDFVSVGSNDLFQFAMAVDRGNARVSERFDILGRPFLRILREIVRAGERNNTPV 677

Query: 757 GVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVL-GLEEA 815
            +CG +AS+ L+   L+GLG   +S+S   +  +KA +  LD      +    L  ++  
Sbjct: 678 TLCGEMASKPLSAMALLGLGFRSVSMSPTAVGPVKAMLLALDAGRLNELLEAALDDVKSD 737

Query: 816 AEVREALRQYHAA 828
             +R+ L  + AA
Sbjct: 738 TSIRQLLVDFAAA 750


Lambda     K      H
   0.318    0.133    0.371 

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: 1136
Number of extensions: 44
Number of successful extensions: 3
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: 838
Length of database: 755
Length adjustment: 41
Effective length of query: 797
Effective length of database: 714
Effective search space:   569058
Effective search space used:   569058
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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