GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuE in Phyllobacterium brassicacearum STM 196

Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_106710601.1 CU102_RS08085 ABC transporter substrate-binding protein

Query= TCDB::Q9R9Q7
         (423 letters)



>NCBI__GCF_003010955.1:WP_106710601.1
          Length = 420

 Score =  598 bits (1541), Expect = e-175
 Identities = 281/423 (66%), Positives = 347/423 (82%), Gaps = 3/423 (0%)

Query: 1   MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLV 60
           M  K FV TL++   +A     A AA+LS+ +  TG    FLR Q+ RFEKETG+KV++V
Sbjct: 1   MIAKSFVTTLLATTLLASG---AFAADLSIVSGDTGNGREFLRKQLDRFEKETGNKVSIV 57

Query: 61  TMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSII 120
            MPA+SS+ F Q+RLWLAAGN D+DVY+TDVIWAPQLA+QF+DL +A KDV+ +H PSII
Sbjct: 58  AMPANSSDNFGQFRLWLAAGNTDIDVYRTDVIWAPQLADQFLDLKDAAKDVIDQHIPSII 117

Query: 121 QSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSAD 180
           +SQTVNGKLVA+P +TDAPALYYRKDLL+KY K  PKTWDE+AATAKE+QD ERAAG+  
Sbjct: 118 ESQTVNGKLVAMPVFTDAPALYYRKDLLEKYKKPVPKTWDEMAATAKEIQDGERAAGNKS 177

Query: 181 IWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAP 240
           I+G+VFQ NAYEGLTCNALEW+KSSGGGQI+E DGTIS+NN  AA A+++ K WI TI+P
Sbjct: 178 IYGYVFQANAYEGLTCNALEWVKSSGGGQIVEADGTISINNPDAAVAIDRAKGWIDTISP 237

Query: 241 KGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSS 300
           KGVLAY EEE+RG+WQTGN+VFMRNWPYAYAL   DDS +KGKF+VAPLP+  +G   ++
Sbjct: 238 KGVLAYTEEEARGIWQTGNSVFMRNWPYAYALAGSDDSTIKGKFDVAPLPSGKEGQNSAA 297

Query: 301 TLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPF 360
           TLGGWN+AVSKYS   E AI    FL SA+ QK RA+  +++PTI +LYDD ++AAAQP 
Sbjct: 298 TLGGWNVAVSKYSKSPEEAIKLALFLSSADEQKARALSQASMPTIKSLYDDKDIAAAQPL 357

Query: 361 MPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKG 420
           +P+WKP+F+++VPRPSA  KVKYNEVS+ FWSAVH+TLSGNGTAA+NLELLE +LTEL+G
Sbjct: 358 IPNWKPVFENSVPRPSAPTKVKYNEVSNMFWSAVHDTLSGNGTAADNLELLEAKLTELQG 417

Query: 421 DAW 423
            +W
Sbjct: 418 GSW 420


Lambda     K      H
   0.313    0.129    0.383 

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: 603
Number of extensions: 16
Number of successful extensions: 1
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: 423
Length of database: 420
Length adjustment: 32
Effective length of query: 391
Effective length of database: 388
Effective search space:   151708
Effective search space used:   151708
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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