GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Erythrobacter gangjinensis K7-2

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_082115713.1 AAW01_RS11260 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= metacyc::MONOMER-12387
         (496 letters)



>NCBI__GCF_001010925.1:WP_082115713.1
          Length = 1202

 Score =  147 bits (372), Expect = 2e-39
 Identities = 127/435 (29%), Positives = 201/435 (46%), Gaps = 46/435 (10%)

Query: 54   EDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALG 113
            E V RA EA    F  W +T    R   +++  +LL +  ++L  L+  EAGK    A+ 
Sbjct: 620  ESVKRAAEA----FPGWSSTSVHERAECLEKAADLLEDRMENLLGLIMREAGKSAPNAIA 675

Query: 114  EVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVGVISAFNFPVAVWAWNA 173
            EV+E +D   +    +R                ++    LG V  IS +NFP+A++    
Sbjct: 676  EVREAVDFLRYYAQQARDS--------------LDGADALGPVVCISPWNFPLAIFVGEV 721

Query: 174  AVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERLVDSP 233
            + AL  G+TV+ KP+E TPL  A    ++     +AG P+ + Q+V G   +G  LV SP
Sbjct: 722  SAALAAGNTVLAKPAEETPLIAAQAIGIMH----EAGVPEDVVQLVPGDGRIGAALVGSP 777

Query: 234  RVPLVSATGSTRMGRAVGPRVAARF--GRT----ILELGGNNAAVVTPSADLDLTVNAAV 287
             +  V+ TGST + + +  ++A R   G +    I E GG NA VV  SA  +  V   V
Sbjct: 778  DICGVTFTGSTEVAKIIQRQLAERLLPGGSPLPFIAETGGQNAMVVDSSALPEQVVRDVV 837

Query: 288  FAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFG 347
             +A  +AGQRC+ LR L +  D+AD +++ L  A   L +G   + +  VGP++   A  
Sbjct: 838  ASAFDSAGQRCSALRVLCLQADVADDMLDMLRGAMAELRVGATDRLSVDVGPVITAEAKE 897

Query: 348  RMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILYVL 407
             +   +E   + G  +    + +  +A     +V P ++ + +   + R E F P+L+V+
Sbjct: 898  TIETHIEDMRSRGFKV---EQLELDEATGYGTFVAPTIIEIDSVDQLGR-EVFGPVLHVV 953

Query: 408  TY--RDLDEAIRLNNEVPQACRQGSRTD--------GAPADDPRCRARRRAGGANCPAVP 457
             Y  +DL + ++  N        G  T          A A+       R   GA     P
Sbjct: 954  RYARKDLPQLMQAINATGYGLTFGLHTRIDETIAQVTAQAEVGNIYVNRNVIGAIVGVQP 1013

Query: 458  ----GRSGTGAGAGG 468
                G SGTG  AGG
Sbjct: 1014 FGGQGLSGTGPKAGG 1028


Lambda     K      H
   0.320    0.135    0.406 

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: 1149
Number of extensions: 55
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: 496
Length of database: 1202
Length adjustment: 41
Effective length of query: 455
Effective length of database: 1161
Effective search space:   528255
Effective search space used:   528255
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: 55 (25.8 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