GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Limnohabitans curvus MWH-C5

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_108401420.1 B9Z44_RS00730 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_003063475.1:WP_108401420.1
          Length = 380

 Score =  452 bits (1163), Expect = e-132
 Identities = 229/374 (61%), Positives = 286/374 (76%), Gaps = 3/374 (0%)

Query: 1   MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60
           M L  KLT VA +AA + +A AQEQVVKIGHVAPVSGA AH GKDNE GAR+AIEELNA+
Sbjct: 1   MHLSFKLTAVATLAALSSLALAQEQVVKIGHVAPVSGAIAHLGKDNEYGARLAIEELNAK 60

Query: 61  GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120
           GV I GKK+K ELVAEDDAADPKQGTAAAQKL DAKV+GV+GHLNSGTTIPASK+Y+D G
Sbjct: 61  GVNINGKKVKLELVAEDDAADPKQGTAAAQKLVDAKVSGVIGHLNSGTTIPASKIYSDAG 120

Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180
           IP ++ ++TNP  T+ GYKT FR++A+D  LG  L  YAV+ LK K++A+IDDRTAYGQG
Sbjct: 121 IPQISPSSTNPKYTRQGYKTAFRVVADDVHLGGTLGRYAVNELKGKSIAVIDDRTAYGQG 180

Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240
           VA+ F+K   A G  +V  +FTTDKATDFM ILT +K K PD IF+GGMD  GGPM++QM
Sbjct: 181 VAEEFEKAVKAAGGNLVGHEFTTDKATDFMPILTTLKGKKPDIIFFGGMDAVGGPMMKQM 240

Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSLAKMPGGTAWKAKYDAK 299
           + LG+   K+ GGDGICT+E+ KLA  A   G V+CAE GG   A   G   + AK+  +
Sbjct: 241 KSLGI-KAKFMGGDGICTNEMIKLAGDAMADGQVVCAEAGGVDGALKKGMDDFSAKFKKR 299

Query: 300 YPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSS-FKGVTSTIAFEPNGEMK 358
           + +  ++YSPY YDA +++VDAM+RA S +P  Y PELAK++ FKGVT TI+F+  G++K
Sbjct: 300 FNDDVKLYSPYVYDAVYVMVDAMQRAKSSEPAKYLPELAKTTGFKGVTGTISFDAKGDIK 359

Query: 359 NPAITLYVYKDGKK 372
           N A+TLY +K GK+
Sbjct: 360 NGALTLYTFKAGKR 373


Lambda     K      H
   0.315    0.131    0.375 

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: 521
Number of extensions: 19
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: 375
Length of database: 380
Length adjustment: 30
Effective length of query: 345
Effective length of database: 350
Effective search space:   120750
Effective search space used:   120750
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: 42 (22.0 bits)
S2: 50 (23.9 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