GapMind for catabolism of small carbon sources

 

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

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

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



>NCBI__GCF_001482365.1:WP_058858173.1
          Length = 566

 Score =  281 bits (719), Expect = 7e-80
 Identities = 217/570 (38%), Positives = 297/570 (52%), Gaps = 41/570 (7%)

Query: 273 GVCASPGSAFGQVVQVTDPELVITEQGTGGATE----RAALTRGLLAANEALQVLQDKAA 328
           GVCA  G   G++V +  P   + E   G A        A+ R   AA E    L+ +A 
Sbjct: 8   GVCA--GRVIGELVSMPAP---VAEPAAGLALRDEAPEDAVARLQEAAAEVKAELKRRAE 62

Query: 329 GSAQ---AEIFRAHQELLEDPTLLEHAHRLLGE-GKSAAFAWNSATLATVTLFQGLGNAL 384
            + +   A++ ++   +  D  LL++A +L+ + G +   A   A  A     + LG  +
Sbjct: 63  AATEKDAADVLKSTALMAGDRALLKNAGKLITDRGLAPERALWEAASAYAEQMRALGGYM 122

Query: 385 IAERAADLADVGQRVLKLILGIQDSAWDLPERA---ILIAEQLTPSQTASLDTRKVLGFV 441
            AERAAD+ DV  R++  + G+      +PER    +L AE L P+ TA+LD  KVL  V
Sbjct: 123 -AERAADIEDVRARLVARLRGLPMPG--IPERETPFVLTAEDLAPADTATLDPAKVLALV 179

Query: 442 TVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLE 501
           T AGG  SH AILAR LGLPAI      V  LA+G +V +D   GE+  EP   E E + 
Sbjct: 180 TSAGGPQSHTAILARNLGLPAIVAARG-VEELADGTEVFVDGATGEVRTEPGAEERELVA 238

Query: 502 AARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFL 561
           +  +    R   D           DG  V + ANV + ++   A   G +GVGLLR+EF 
Sbjct: 239 SWERAAAARSDFDGR-----GVLADGTEVPLYANVGTAEDARTAAAAGAQGVGLLRTEFC 293

Query: 562 YLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRG 621
           +L R   PS EEQ   YTAI  A   E+ +VVRTLD G DKPL ++   AE NP LG+RG
Sbjct: 294 FLGRGEEPSVEEQVEQYTAIFAAF-EEKKVVVRTLDAGADKPLPFLTDTAEPNPALGVRG 352

Query: 622 IRLCLERPQLLREQFRAILAS--AGFARLHIMLPMVSLLSELHLARKILEEEALALGLTE 679
            R     P +L  Q  AI  +  A  A + +M PM+S   E   AR      A A GL  
Sbjct: 353 YRTDRSVPGVLARQLEAIARADEATAAEVWVMAPMISAAEE---ARDFAAMAATA-GL-R 407

Query: 680 LPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVL 739
           +P  G+M+E PSAA+ AD    HV+F S+GTNDLTQYT+A DR    LA   + + PAVL
Sbjct: 408 VP--GVMVETPSAAVTADQILRHVEFVSLGTNDLTQYTMAADRMLGSLAELNNPWQPAVL 465

Query: 740 RLIATTVKAAH------AHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKAT 793
           R++  TV+ A       A  + VGVCG  A++     VL+GLGV  LS+S   +  + A 
Sbjct: 466 RMVRLTVEGARRAEAEGAGRRNVGVCGEAAADPALAVVLVGLGVHTLSMSPRALSPVAAV 525

Query: 794 VRELDLADCQIIARQVLGLEEAAEVREALR 823
           +R +DLA  + +A   +    AAE   A+R
Sbjct: 526 LRSVDLATARSLAELAVEQATAAEAAAAVR 555


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: 989
Number of extensions: 52
Number of successful extensions: 7
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: 566
Length adjustment: 39
Effective length of query: 799
Effective length of database: 527
Effective search space:   421073
Effective search space used:   421073
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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