GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Pseudomonas stutzeri RCH2

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__psRCH2:GFF2021
          Length = 553

 Score =  163 bits (412), Expect = 1e-44
 Identities = 93/270 (34%), Positives = 161/270 (59%), Gaps = 4/270 (1%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP- 103
           ++EV +L V +  G  ++ + V  V+F + KGE L ++GESGSGK+    +ILR +  P 
Sbjct: 10  LVEVRDLAVEFVTGE-QVQRVVEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLPYPL 68

Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163
            +   G+++F+G D+        RK+    I+ V Q    +LNP+  + +        H 
Sbjct: 69  ARHPQGQILFHGQDLLKADEKAMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEVLEIHK 128

Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222
               K    R  ELL+LVG+ +P + ++ YP +LSGG +QRV+IA++L   P+L++ DEP
Sbjct: 129 GLRGKAATARTLELLELVGIPEPRKRIRAYPHELSGGQRQRVVIAMALANEPELLIADEP 188

Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282
           T+ALD+  Q  +L+L+K +   +G+ ++ ++HD+  + +IA+R+ VM +G V+E+   E+
Sbjct: 189 TTALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQRGRVVEQALCED 248

Query: 283 IIKSPLNPYTSLLVSSIPSLKGEVKVINVP 312
           + ++P +PYT  L+++ PS  G V V   P
Sbjct: 249 LFRAPQHPYTQELLAAEPS-GGPVAVEEAP 277



 Score =  146 bits (368), Expect = 1e-39
 Identities = 86/236 (36%), Positives = 141/236 (59%), Gaps = 7/236 (2%)

Query: 63  IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122
           IKAV+ V+F + KG+ LGI+GESGSGK+TL  AILR +   G+I      F G  + SM+
Sbjct: 303 IKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAILRLLGSRGEIR-----FQGQHLQSMS 357

Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182
             + R L  + +  V Q    +L+P + + +I       H   + K   +   E L  VG
Sbjct: 358 QRQVRPLR-RQMQVVFQDPFGSLSPRMSVGQIVGEGLHIHRMGNAKEQEQAIIEALVEVG 416

Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242
           LDP      YP + SGG +QR+ IA +L+L P LIL+DEPTSALD   Q  +++L++++ 
Sbjct: 417 LDP-ETRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSALDRTVQRQVVELLRSLQ 475

Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298
            +  +T ++++HD+  +  ++++++V+ +G V+E+G   +I  +P +PYT  L+ S
Sbjct: 476 AKYNLTYLFISHDLAVVRALSHQMMVVKQGQVVEQGAAADIFAAPQHPYTQQLLES 531


Lambda     K      H
   0.319    0.138    0.391 

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: 414
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 362
Length of database: 553
Length adjustment: 33
Effective length of query: 329
Effective length of database: 520
Effective search space:   171080
Effective search space used:   171080
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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