GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Kocuria flava HO-9041

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_058858173.1 AS188_RS06525 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>NCBI__GCF_001482365.1:WP_058858173.1
          Length = 566

 Score =  313 bits (802), Expect = 2e-89
 Identities = 227/574 (39%), Positives = 310/574 (54%), Gaps = 39/574 (6%)

Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGD-----RLHEALSLTRQNLKALADDT 337
           G+    G  IG +  +P A V+ P   + L +        RL EA +  +  LK  A+  
Sbjct: 6   GVGVCAGRVIGELVSMP-APVAEPAAGLALRDEAPEDAVARLQEAAAEVKAELKRRAEAA 64

Query: 338 ARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVE-GHGVAWSWHQAVERTAAGLAALDNP 396
             +     A +  + A +  D  L+  A +L+ + G     +  +A    A  + AL   
Sbjct: 65  TEK---DAADVLKSTALMAGDRALLKNAGKLITDRGLAPERALWEAASAYAEQMRALGG- 120

Query: 397 VLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGL 456
            +A RAAD+ DV  R++AR+   L   G P+  +TP +L AEDL+P+DTA LD A+V+ L
Sbjct: 121 YMAERAADIEDVRARLVARLR-GLPMPGIPER-ETPFVLTAEDLAPADTATLDPAKVLAL 178

Query: 457 ATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADA 516
            T+ GGP SHTAILAR LGLPA+VA    + ELA+GT   +DG +G +   P A +    
Sbjct: 179 VTSAGGPQSHTAILARNLGLPAIVAA-RGVEELADGTEVFVDGATGEVRTEPGAEERELV 237

Query: 517 RAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEF 576
            +W  R  A +++ + R  L     DG EV + ANV   +    A + GA+ VGL+RTEF
Sbjct: 238 ASW-ERAAAARSDFDGRGVLA----DGTEVPLYANVGTAEDARTAAAAGAQGVGLLRTEF 292

Query: 577 LFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRG 636
            FL RG+ P  +EQ E Y  +  A E + ++VR LD G DK +P L    E NP LGVRG
Sbjct: 293 CFLGRGEEPSVEEQVEQYTAIFAAFEEKKVVVRTLDAGADKPLPFLTDTAEPNPALGVRG 352

Query: 637 ARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAEL 696
            R     P +L  QL A+ RA +   A+    + +M PMI+A  E +   A      A L
Sbjct: 353 YRTDRSVPGVLARQLEAIARADEATAAE----VWVMAPMISAAEEARDFAAMA--ATAGL 406

Query: 697 DAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHP 756
             P    G+MVE P+AA+ AD + RHV+F S+GTNDLTQY +A DR    LA   +   P
Sbjct: 407 RVP----GVMVETPSAAVTADQILRHVEFVSLGTNDLTQYTMAADRMLGSLAELNNPWQP 462

Query: 757 AVLRLIRLTVEGAER------HGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAV 810
           AVLR++RLTVEGA R        R VGVCG  A DP  A +L GLGV  LSM+PR +  V
Sbjct: 463 AVLRMVRLTVEGARRAEAEGAGRRNVGVCGEAAADPALAVVLVGLGVHTLSMSPRALSPV 522

Query: 811 KDRLRGSDLSALKDAAQRALD----CETADAVRA 840
              LR  DL+  +  A+ A++     E A AVRA
Sbjct: 523 AAVLRSVDLATARSLAELAVEQATAAEAAAAVRA 556


Lambda     K      H
   0.319    0.134    0.387 

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: 1072
Number of extensions: 54
Number of successful extensions: 6
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: 846
Length of database: 566
Length adjustment: 39
Effective length of query: 807
Effective length of database: 527
Effective search space:   425289
Effective search space used:   425289
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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