GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Marinobacter adhaerens HP15

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF4122 HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein

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



>FitnessBrowser__Marino:GFF4122
          Length = 373

 Score =  241 bits (615), Expect = 2e-68
 Identities = 116/248 (46%), Positives = 174/248 (70%), Gaps = 2/248 (0%)

Query: 4   LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63
           L LS++ K +GG  V+ G+DL+I  GEF+  +GPSGCGK+TLLR++AG E    G +T+ 
Sbjct: 6   LSLSNLSKQFGGKTVLDGLDLEIYDGEFITLLGPSGCGKTTLLRLMAGFEHPDEGTITLA 65

Query: 64  DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123
              +    P  R +  VFQ YAL+PHM+V +N+ + L+    P+ EI +RV+EA  +++L
Sbjct: 66  GENLTHTAPENRPLNTVFQHYALFPHMSVFDNVAYGLKMEKRPKDEIRQRVDEALAMVQL 125

Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183
                RKP QLSGGQ+QRVAI RA+V+ P++ L DEPLS LD +LR  M++E+ RL ++L
Sbjct: 126 QDFARRKPHQLSGGQQQRVAIARAVVKRPRLLLLDEPLSALDYKLRRTMQVELKRLQREL 185

Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243
             T V+VTHDQ EA++++D++VV++ G+V+Q+G+P ++Y+ PANLF A F+G  + NF  
Sbjct: 186 GITFVFVTHDQEEALSMSDRVVVLKDGLVQQLGTPREVYERPANLFTARFVG--ETNFFP 243

Query: 244 GVIEIDED 251
           G +E  +D
Sbjct: 244 GTVESVQD 251


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: 340
Number of extensions: 11
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: 358
Length of database: 373
Length adjustment: 30
Effective length of query: 328
Effective length of database: 343
Effective search space:   112504
Effective search space used:   112504
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 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:

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