GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Phyllobacterium brassicacearum STM 196

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_106709178.1 CU102_RS01465 ATP-binding cassette domain-containing protein

Query= TCDB::Q9WXN5
         (330 letters)



>NCBI__GCF_003010955.1:WP_106709178.1
          Length = 329

 Score =  183 bits (464), Expect = 6e-51
 Identities = 108/296 (36%), Positives = 171/296 (57%), Gaps = 20/296 (6%)

Query: 19  KVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEF 78
           K  + AV+G+   + + EV+G+VGESGCGK+TL+ ++ + ++ P +       +R +G  
Sbjct: 24  KRKLHAVNGIDLTLEKGEVLGIVGESGCGKSTLARIL-LGLLPPTSGT-----IRFDGRD 77

Query: 79  VELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEE-ELLDKA 137
           +         +KR+   +++  + Q   ++L P   +   V    + HGI    +   +A
Sbjct: 78  LRT-------LKRRDLARQVQPVFQDPYSSLNPRRTIASIVAFPLDVHGIGSSADRRREA 130

Query: 138 RRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLL 197
            +  + VGL   +  R+P ELSGG RQR  IA A I+ P +++ DEPTSALDV  Q  +L
Sbjct: 131 LKIMDLVGLPARFADRHPRELSGGQRQRVAIARALIMKPEIIVCDEPTSALDVSVQSQIL 190

Query: 198 KVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQG 257
            +L++++ +    + +FI+H++  V  IA R+ +MY G++VE A   ++   P HPYT+ 
Sbjct: 191 NLLLELRNE-FGLTYVFISHNLGVVEHIATRVAVMYLGRVVELAETSAMFANPRHPYTRA 249

Query: 258 LFNSVLTPEPEVKKRGI--TTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPL 311
           L +S+LTP P +   GI  T +  A P+ +NPPSGC FHPRCP A D CK  EP L
Sbjct: 250 LLSSILTPVPGL---GIPETGLGLAFPDPLNPPSGCVFHPRCPSAFDACKCVEPQL 302


Lambda     K      H
   0.321    0.138    0.405 

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: 307
Number of extensions: 16
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: 330
Length of database: 329
Length adjustment: 28
Effective length of query: 302
Effective length of database: 301
Effective search space:    90902
Effective search space used:    90902
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: 49 (23.5 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