GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__Cola:Echvi_1582
          Length = 225

 Score =  132 bits (331), Expect = 8e-36
 Identities = 86/225 (38%), Positives = 134/225 (59%), Gaps = 13/225 (5%)

Query: 14  IIQMQGVNKWYGQ----FHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69
           I+ ++ V+K Y        VL+DINL+VK G+ I + GPSGSGK+T +     L+    G
Sbjct: 3   ILSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSG 62

Query: 70  RIVVDGVELTN-DLKQIEAIR-REVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE 127
            + ++G  L      Q  A+R +E+G +FQ+F L P LT L+N  + P+ ++K  ++ A+
Sbjct: 63  SVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALEN-VMVPLELKK--RKDAK 119

Query: 128 EIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKE 187
           + A   L++V + ++   YP QLSGG+QQRV+IARA   +PKI+  DEPT  LD E   E
Sbjct: 120 QKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGE 178

Query: 188 VLDTMIGLAED--GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQ 230
           +++T+I       G T++ VTH+   A    NR+I +  G+I E+
Sbjct: 179 LIETLIFDLNKALGTTLILVTHDTDLA-AKTNRIIHIKGGKIQEE 222


Lambda     K      H
   0.322    0.137    0.407 

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: 139
Number of extensions: 7
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: 254
Length of database: 225
Length adjustment: 23
Effective length of query: 231
Effective length of database: 202
Effective search space:    46662
Effective search space used:    46662
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 (21.9 bits)
S2: 46 (22.3 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