GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Halococcus hamelinensis 100A6

Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate WP_152416156.1 C447_RS11610 ATP-binding cassette domain-containing protein

Query= reanno::pseudo5_N2C3_1:AO356_09895
         (257 letters)



>NCBI__GCF_000336675.1:WP_152416156.1
          Length = 233

 Score =  149 bits (377), Expect = 4e-41
 Identities = 90/221 (40%), Positives = 124/221 (56%), Gaps = 11/221 (4%)

Query: 9   EIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVAG 68
           ++R  +   G +E L GVSL+  DG   +++G SGSGKST L  +  L+ P  G + VAG
Sbjct: 5   DVRKTYDLGGTVEALAGVSLSLADGSYTAVMGPSGSGKSTLLNLVGALDTPTDGTVEVAG 64

Query: 69  EELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQSKA 128
            +L   AA + E  A  G       +EIGFVFQ FNL P    ++N+   P    G S+ 
Sbjct: 65  NDLG--AATDDERAAIRG-------TEIGFVFQTFNLLPRSDAVENVA-LPLVFAGWSRE 114

Query: 129 EAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEM 188
              E A  LL +VG+ D+RH  P +LSGGQ+QR AIAR LA  P V+L DEPT  +D E 
Sbjct: 115 RRHERATELLDRVGLGDRRHHRPTQLSGGQRQRVAIARALAPDPAVVLADEPTGNVDTET 174

Query: 189 VQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQG 229
              V++++ A  + G T+LLVTH    A   +  +V +  G
Sbjct: 175 GAGVMNLLAAANDRGTTILLVTHSREIAEH-ADRIVTVRDG 214


Lambda     K      H
   0.317    0.132    0.363 

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: 116
Number of extensions: 4
Number of successful extensions: 3
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: 257
Length of database: 233
Length adjustment: 24
Effective length of query: 233
Effective length of database: 209
Effective search space:    48697
Effective search space used:    48697
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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