GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1894 in Halomonas desiderata SP1

Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate WP_086510781.1 BZY95_RS15410 carbohydrate ABC transporter substrate-binding protein

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



>NCBI__GCF_002151265.1:WP_086510781.1
          Length = 422

 Score =  446 bits (1146), Expect = e-130
 Identities = 225/430 (52%), Positives = 301/430 (70%), Gaps = 14/430 (3%)

Query: 2   NAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTW 61
           N   + A  ++ A+ ++L  S+ AAE    VEV+HWWTSGGE  A +VLK  +E +G+ W
Sbjct: 6   NPFRKTALALATAAAASLTFSIQAAE----VEVLHWWTSGGEARAANVLKELMEAEGYGW 61

Query: 62  KDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENW 121
           +D AVAGGGG TAMTVLKSRA++GNPP  AQIKGP+IQEWG  GLL    L +V++AE W
Sbjct: 62  EDFAVAGGGGETAMTVLKSRAMSGNPPSAAQIKGPEIQEWGELGLLGE--LDEVAEAEGW 119

Query: 122 DGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKL 181
           D LL   V+D +++ G YVAVPVN+HRVNWLW NP+V   AG+E  PTTL+E +AAG+ +
Sbjct: 120 DELLPPTVADVMRHNGSYVAVPVNVHRVNWLWANPQVLAAAGVEM-PTTLDELFAAGEAI 178

Query: 182 KAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKK 241
           + AG+I LAHGGQ WQD+TVFE V+L+  G + Y++ALV+LD + L    M ++    K+
Sbjct: 179 REAGYIPLAHGGQAWQDATVFESVLLASGGTEFYQQALVELDPEALGSERMIEALETFKR 238

Query: 242 ITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEK 301
           +   MD + +GRDWNIA + VI G AGMQ+MGDWAK E+TAA   AG++Y C A PGT+ 
Sbjct: 239 LRELMDADMSGRDWNIATSMVIEGSAGMQLMGDWAKGEFTAAGLTAGEEYLCAAAPGTQD 298

Query: 302 AFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDK 361
           AFT+NIDS+A+F+++ + +    AQQ LA++ L   FQ+ F++ KGSIP R D    +D 
Sbjct: 299 AFTFNIDSLAMFRVEGEER---EAQQALARLVLEPTFQEAFNLAKGSIPARPD----LDM 351

Query: 362 LGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKAS 421
            GFD CAQ+S  DF    + GGL PSMAH MA    VQGAIFDVVTN+ N +D    +A+
Sbjct: 352 SGFDVCAQQSMDDFQRTAEEGGLVPSMAHGMAVRADVQGAIFDVVTNYFNSRDMAAEEAA 411

Query: 422 AQLASAVKAA 431
            ++ +A +AA
Sbjct: 412 RRMVNAAQAA 421


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: 516
Number of extensions: 17
Number of successful extensions: 5
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: 422
Length adjustment: 32
Effective length of query: 400
Effective length of database: 390
Effective search space:   156000
Effective search space used:   156000
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 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