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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2062 ABC-type sugar
           transport system, periplasmic component
          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.

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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:

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, or view the source code.

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