GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  244 bits (623), Expect = 3e-69
 Identities = 124/283 (43%), Positives = 182/283 (64%), Gaps = 2/283 (0%)

Query: 2   SELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLT 61
           S ++L  V K + G  V+  V LDI+ GEF+  +GPSGCGK+TLLR++AG E  SSG++ 
Sbjct: 6   SVIRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65

Query: 62  IDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHIL 121
           +D   M DV P  R +  VFQSYAL+PHM+V +N+ F LR +G+P+ EI +RV +A  ++
Sbjct: 66  LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125

Query: 122 ELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHK 181
            L     R+P  LSGGQ+QRVAI RA+V  P + L DEPLS LD +LRV MR E+ +L +
Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185

Query: 182 QLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNF 241
           ++  T ++VTHDQ EA +++D++VVM  G V QVG+P+++Y+ P N+FVA F+G  + N 
Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVG--ETNV 243

Query: 242 LKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPE 284
            +GV    +      L +    ++        G  + + +RPE
Sbjct: 244 FEGVAGQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPE 286


Lambda     K      H
   0.321    0.139    0.396 

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: 358
Number of extensions: 16
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 370
Length adjustment: 29
Effective length of query: 329
Effective length of database: 341
Effective search space:   112189
Effective search space used:   112189
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: 49 (23.5 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