GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Paucidesulfovibrio gracilis DSM 16080

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  246 bits (627), Expect = 1e-69
 Identities = 136/293 (46%), Positives = 184/293 (62%), Gaps = 15/293 (5%)

Query: 4   VLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLY 63
           + LEH+ K + G+T   + D  LDI+  EF   +GPSGCGKTT LR++AG E  + G + 
Sbjct: 8   IRLEHVAKEFDGET--VLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65

Query: 64  IGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKIL 123
           +  R + DVPP  R +  VFQ+YAL+PHM+V+ N+AFGL++  +PK EI  RV +A +++
Sbjct: 66  LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125

Query: 124 DIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQ 183
            +A    R+P +LSGGQ+QRVA+ RA+V  P V L+DEPLS LD KLRVQMR E+++L +
Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185

Query: 184 RLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNF 243
            +  T I+VTHDQ EA +M DR+VVM +G + Q  TP  VY QP NMFVA F+G    N 
Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE--TNV 243

Query: 244 IRGEIVQ-DGDAFYFRAPSISLRLPEGRYGVLKASGAI--GKPVVLGVRPEDL 293
             G   Q DG         I   L EGR   L +      G  + + +RPEDL
Sbjct: 244 FEGVAGQSDG--------GILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL 288


Lambda     K      H
   0.321    0.138    0.395 

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: 392
Number of extensions: 18
Number of successful extensions: 1
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: 384
Length of database: 370
Length adjustment: 30
Effective length of query: 354
Effective length of database: 340
Effective search space:   120360
Effective search space used:   120360
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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