GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1894 in Acidovorax sp. GW101-3H11

Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_2062 ABC-type sugar transport system, periplasmic component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894
         (432 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2062
          Length = 416

 Score =  426 bits (1096), Expect = e-124
 Identities = 223/414 (53%), Positives = 279/414 (67%), Gaps = 12/414 (2%)

Query: 18  ALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGSTAMTV 77
           A+ L+   + S G VEV+H+WTSGGE  +V  LK  ++  G TW+D AVAGGGG +AMTV
Sbjct: 11  AVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAMTV 70

Query: 78  LKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSDTVKYEG 137
           LKSR ++GNPP  AQ KGP IQEW S G+L+   +  ++KAE WD LL K V+D +KY+G
Sbjct: 71  LKSRVISGNPPSAAQTKGPAIQEWASEGVLAN--MDTLAKAEKWDELLPKVVADVMKYKG 128

Query: 138 DYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAHGGQPWQ 197
            YVA PVN+HRVNW+W + E  KKAG+   P T +EF+AA DKLKAAG + +AHGGQ WQ
Sbjct: 129 AYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQ 188

Query: 198 DSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNRAGRDWNI 257
           D T FE VVL V GA  Y+ ALV LD   L+   M KS    ++I GY DP   GRDWN+
Sbjct: 189 DFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNL 248

Query: 258 AAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSMAVFKLK- 316
           A A +I GKAG Q+MGDWAK E+ AA K  GKD+ C A PG+  AFT+N+DS  +FKLK 
Sbjct: 249 ATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKD 308

Query: 317 -ADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQKSAKDF 375
            A +K    AQ DLA   +   FQ+VF++NKGSIPVR      MDK  FD+CA+ SAKDF
Sbjct: 309 AAAQK----AQSDLASSIMSPAFQEVFNLNKGSIPVRAG--QPMDK--FDDCAKASAKDF 360

Query: 376 IADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVK 429
           +   K+GGL PS AH MA + A +GAI DVV+ F ND     A A  ++A+A K
Sbjct: 361 VDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAK 414


Lambda     K      H
   0.314    0.129    0.377 

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: 611
Number of extensions: 25
Number of successful extensions: 4
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: 432
Length of database: 416
Length adjustment: 32
Effective length of query: 400
Effective length of database: 384
Effective search space:   153600
Effective search space used:   153600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 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