GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

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



>FitnessBrowser__Korea:Ga0059261_1321
          Length = 238

 Score =  139 bits (349), Expect = 7e-38
 Identities = 90/237 (37%), Positives = 129/237 (54%), Gaps = 16/237 (6%)

Query: 1   MAQATPALEIRNLHKRYGQ----LEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLL 56
           +A A P + +RN+ K +G+     + LKGV L   + D ++++G SGSGKST +  +  L
Sbjct: 1   VADADPIIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCL 60

Query: 57  ENPNQGQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNII 116
           + P  G+ L  G  +        E +  D + + R R  +GFVFQ FNL    + L+N+ 
Sbjct: 61  DVPTSGEFLFKGVYI--------ETLDRDQRALVR-RKYLGFVFQGFNLLSRTNALENV- 110

Query: 117 EAPRRVLGQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVIL 176
           E P    G+ K    E+  A L KVG+AD     PAELSGGQ QR AIAR +   P V+L
Sbjct: 111 ELPLLYRGEDKKVRHELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLL 170

Query: 177 FDEPTSALDPEMVQEVLSVIRAL-AEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVE 232
            DEPT  LD     E++ ++ +L  + G T+L+VTHE   A   +  +V    GLVE
Sbjct: 171 ADEPTGNLDSARSVEIMELLTSLNKDSGITVLMVTHEPDMA-AFARTIVHFKDGLVE 226


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: 120
Number of extensions: 7
Number of successful extensions: 4
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: 238
Length adjustment: 24
Effective length of query: 233
Effective length of database: 214
Effective search space:    49862
Effective search space used:    49862
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 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