GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Pseudomonas stutzeri RCH2

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__psRCH2:GFF4241
          Length = 335

 Score =  172 bits (435), Expect = 2e-47
 Identities = 95/249 (38%), Positives = 146/249 (58%), Gaps = 2/249 (0%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           ++   L I  GE+F ++G SG+GKST++RL+NRL EP+ G++L++G D+  +    LR  
Sbjct: 21  LQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNGEDVTALDADGLRRF 80

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDAL-RQVGLENYAHSYP 162
           R++ + M+FQ F L+   TV DN A  + LAGI +    +  + AL  +VGL+ +A  YP
Sbjct: 81  RQR-VGMIFQHFNLLMSKTVADNVAMPLRLAGIRSRREIDARVAALLERVGLKEHARKYP 139

Query: 163 DELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFIS 222
            +LSGG +QRVG+ARALA  P ILL DEA SALDP     +   L ++  + + TIV I+
Sbjct: 140 AQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLIT 199

Query: 223 HDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARR 282
           H++D   R+ DR+A+M  G +V+ G   E+  +P +   + F    +        D    
Sbjct: 200 HEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKHPTTQRFVLEDEAMDESELHDDFAH 259

Query: 283 TPNGLIRKT 291
            P  ++R T
Sbjct: 260 VPGRILRLT 268


Lambda     K      H
   0.319    0.137    0.378 

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: 313
Number of extensions: 17
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: 400
Length of database: 335
Length adjustment: 30
Effective length of query: 370
Effective length of database: 305
Effective search space:   112850
Effective search space used:   112850
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 (21.7 bits)
S2: 49 (23.5 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