GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Pseudomonas putida KT2440

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PP_3948 PP_3948 nicotinate dehydrogenase subunit B

Query= reanno::WCS417:GFF2133
         (447 letters)



>FitnessBrowser__Putida:PP_3948
          Length = 1187

 Score =  247 bits (631), Expect = 1e-69
 Identities = 154/417 (36%), Positives = 213/417 (51%), Gaps = 32/417 (7%)

Query: 6    FARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVAC 65
            F   AG       + A  L W     P TP        ++  A++ RG  VA   DC  C
Sbjct: 766  FGSLAGVFGAALGMLATALPWRAEIAPVTP----PGVGSWSAAMLERGRQVAAAGDCAVC 821

Query: 66   HSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYP 125
            H+++G    AGGL M TP G +++TNITPD  TGIG +S A F+RA+R G++  GR LYP
Sbjct: 822  HTVSGGKANAGGLAMDTPFGTLYSTNITPDPETGIGRWSFAAFERAMREGISRDGRHLYP 881

Query: 126  AMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTAT 185
            A PY S+  ++D D++ALYA+ M    P  Q    + + +P N R  +A WN  F     
Sbjct: 882  AFPYTSFRNINDADMQALYAYLMSQ-TPVRQEAPANQMRFPFNQRPLMAGWNARFLQRGE 940

Query: 186  YAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPS 245
            Y   P + A WNRGAY+V G GHC +CH+PR L   EK     G+ +LAG ++DGW AP+
Sbjct: 941  YQPDPQRSAQWNRGAYLVDGLGHCTACHSPRNLMGAEK----GGSSYLAGGMVDGWEAPA 996

Query: 246  LRQDPNTGLGR----WSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA 300
            L       LG+    WSE ++  +L TG    H V  G M    +     +   D+ AIA
Sbjct: 997  L-----NALGKSSTPWSEDELFNYLSTGFSEKHGVAAGPMGPVVSELAT-LPKSDVRAIA 1050

Query: 301  RYLKSLPGDPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGAT 360
             YL SL G+PQ   A    Q    V  + G   +   C  CH  DG G     P L G +
Sbjct: 1051 HYLSSLEGEPQALAANAAPQVDTHVSLSNGERVFKGACLGCHS-DGLG-----PKLFGVS 1104

Query: 361  SALAKESASAINITLNGSQRVVASGVP-----DAYRMPAFREQLSDTEIAEVLSYVR 412
             ++A  S    ++  N   RVV  G+P     D   MP F++ LSD ++A++ +Y+R
Sbjct: 1105 PSMAVNSNVHSDLPDN-LLRVVLHGIPTPATRDLGYMPGFKDSLSDRQVADLAAYLR 1160


Lambda     K      H
   0.318    0.133    0.423 

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: 1500
Number of extensions: 78
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: 447
Length of database: 1187
Length adjustment: 40
Effective length of query: 407
Effective length of database: 1147
Effective search space:   466829
Effective search space used:   466829
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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