GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araUsh in Phyllobacterium brassicacearum STM 196

Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate WP_106712861.1 CU102_RS19525 ABC transporter substrate-binding protein

Query= uniprot:A0KWY4
         (313 letters)



>NCBI__GCF_003010955.1:WP_106712861.1
          Length = 318

 Score =  350 bits (899), Expect = e-101
 Identities = 178/314 (56%), Positives = 231/314 (73%), Gaps = 3/314 (0%)

Query: 1   MKHNKIITALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADA 60
           MK   + + + +    A  A   TVGFSQ+GSESGWR + +   K EAK+R IDLK ADA
Sbjct: 1   MKRILLASTVAMSFAGAASASDLTVGFSQIGSESGWRAAETSVSKIEAKKRSIDLKIADA 60

Query: 61  QQKQENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL 120
           QQKQENQIKA+R F+AQGVDAI +APVV TGW  VL EAK A+IPV+++DR I+  ++ L
Sbjct: 61  QQKQENQIKAIRGFVAQGVDAIFVAPVVATGWDTVLAEAKEAEIPVILLDRTIETANNDL 120

Query: 121 FLTRIASDFSEEGRKIGQWLMDKTQGN-CDIAELQGTVGATAAIDRAAGFNQVIANYPNA 179
           +LT + SD   EG+  G WL+  T G  C++ ELQGTVG++ AI+R  GF + IA+  N 
Sbjct: 121 YLTAVTSDTVHEGKVAGDWLVKTTAGKPCNVVELQGTVGSSPAINRKKGFEEGIASASNI 180

Query: 180 KIVRSQTGEFTRAKGKEVMEGFLKAQN-GQPLCAVWSHNDEMALGAVQAIKEAGLKPGKD 238
           KI RSQTG+FTRAKGKEVMEGFLKA+N G+ +CA+++HND+MA+GA+QAIKEAGLKPGKD
Sbjct: 181 KITRSQTGDFTRAKGKEVMEGFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKPGKD 240

Query: 239 ILIVSVDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVF 298
           IL+VS+D VPD FKAM++G+ NATVEL+P + GPAFDA+ AY    K   K I T   ++
Sbjct: 241 ILVVSIDAVPDIFKAMSEGEANATVELTPNMAGPAFDALKAYKDSGKAPPKWIQTESKLY 300

Query: 299 TQ-ETAAAEYEKRR 311
           TQ +     YE+++
Sbjct: 301 TQADDPKKVYEEKK 314


Lambda     K      H
   0.316    0.131    0.376 

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: 324
Number of extensions: 12
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: 313
Length of database: 318
Length adjustment: 27
Effective length of query: 286
Effective length of database: 291
Effective search space:    83226
Effective search space used:    83226
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 (21.6 bits)
S2: 48 (23.1 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