GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacC in Pseudomonas putida KT2440

Align Gluconolactonase (characterized, see rationale)
to candidate PP_1170 PP_1170 Gluconolactonase

Query= uniprot:A0A165IRV8
         (316 letters)



>FitnessBrowser__Putida:PP_1170
          Length = 293

 Score =  166 bits (421), Expect = 5e-46
 Identities = 106/294 (36%), Positives = 143/294 (48%), Gaps = 11/294 (3%)

Query: 28  VIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAP 87
           ++   N  GE  +W   EQA+YWVDI  R+LHRW  A G HQ W  DE ++ IA      
Sbjct: 6   IVDARNGTGESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIARSGQ-- 63

Query: 88  GFIVTLRRGFALFDPATD--MAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSM--DFAC 143
           G++  +  G        D  +  R L   +  +AG RFNDG+CD QGRFWAG+M  D   
Sbjct: 64  GWVAGMESGIFQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLLDMQQ 123

Query: 144 EAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATG 203
            A  GALYR+D +G      DG  V NG  +S  G+   +  +       + +D D  +G
Sbjct: 124 GAHVGALYRHDGEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYDTDSG 183

Query: 204 TVSNKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGR-VRLPVSQ 262
           T   K L+       G PDG   D  G  WI   G      H       L R + +PV +
Sbjct: 184 TPHGKHLFVDMRNYPGRPDGAAIDQDGCYWIC--GNDAGQIHRFTPEGRLDRSLSVPVKK 241

Query: 263 VTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPFGG 316
              CAFGGA L  L+++S R   T   L+ +PLAG +FA+D  + GL    + G
Sbjct: 242 PAMCAFGGASLDILYVTSIRP--TGIDLSDQPLAGGVFALDPGTKGLEEPAYRG 293


Lambda     K      H
   0.321    0.137    0.457 

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: 406
Number of extensions: 26
Number of successful extensions: 6
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: 316
Length of database: 293
Length adjustment: 27
Effective length of query: 289
Effective length of database: 266
Effective search space:    76874
Effective search space used:    76874
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: 48 (23.1 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