GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Flavobacterium ummariense DS-12

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_091526344.1 BM253_RS16085 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_900115115.1:WP_091526344.1
          Length = 304

 Score = 94.4 bits (233), Expect = 3e-24
 Identities = 70/223 (31%), Positives = 107/223 (47%), Gaps = 23/223 (10%)

Query: 21  LNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLY-QPDTGTFELDGKPYSPSAPHEVAK 79
           L+ V I +    IYG +GPNGAGK+T   +ITGL  + + G   L GKP     P   ++
Sbjct: 19  LDKVSIQVPEKSIYGFLGPNGAGKSTTIRLITGLLGEQNPGQISLFGKPLEEQLPFAFSQ 78

Query: 80  AGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKSQKLLD 139
            G     +   L+G +T LE++                F  K    +E+   E    +LD
Sbjct: 79  IGCI--IETPTLYGHLTGLEHLK---------------FVAKLQNTDESKFNE----VLD 117

Query: 140 FVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRELLVKI 199
            VG+       ++  S G ++RL IA AL  DP+LL LDEP  G++    + +R LL K+
Sbjct: 118 LVGLDHAKNIKSKKYSLGMKQRLSIAMALINDPKLLILDEPVNGLDPQGIIEMRLLLQKL 177

Query: 200 QAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241
             E G TI +  H +  +  LC  + +L  G    +G  +D++
Sbjct: 178 NREKGITIFISSHILAEVEKLCTHVGILYNGILQFQGTMSDLK 220


Lambda     K      H
   0.320    0.138    0.394 

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: 178
Number of extensions: 12
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 304
Length adjustment: 25
Effective length of query: 230
Effective length of database: 279
Effective search space:    64170
Effective search space used:    64170
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 (21.8 bits)
S2: 47 (22.7 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