GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Dyella japonica UNC79MFTsu3.2

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

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



>FitnessBrowser__Dyella79:N515DRAFT_4232
          Length = 1074

 Score =  159 bits (403), Expect = 4e-43
 Identities = 142/435 (32%), Positives = 200/435 (45%), Gaps = 32/435 (7%)

Query: 56   VDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALGEV 115
            V++A+  A  A   W   PA  R A+++   E L   + +   L   EAGK   +A+ E+
Sbjct: 619  VEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCVREAGKGLPDAIAEI 678

Query: 116  QEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPL---GVVGVISAFNFPVAVWAWN 172
            +E  D   +   ++R+ +G+  P + PG         L   GV   IS +NFP+A++   
Sbjct: 679  REAADFLRYYATMARRYFGQ--PEQLPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQ 736

Query: 173  AAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVG-AADVGERLVD 231
             A AL  G++V+ KP+E T L   A   LL     +AG P  + Q + G  A VG  L  
Sbjct: 737  VAAALAAGNSVIAKPAEQTSLIGHAAVQLLH----EAGVPADVLQYLPGDGATVGAALTR 792

Query: 232  SPRVPLVSATGSTRMGRAVGPRVAAR---FGRTILELGGNNAAVVTPSADLDLTVNAAVF 288
             PRV  V+ TGST    A+   +AAR       I E GG NA +   SA  +  V  AV 
Sbjct: 793  DPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGGQNAMIADSSALPEQIVKDAVS 852

Query: 289  AAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGR 348
            +A  +AGQRC+  R L V EDIAD V   L  A   L +GDP Q +T VGP+++E A   
Sbjct: 853  SAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTDVGPVIDEDARKI 912

Query: 349  MREAVERATAEGGTLCAGGERQFPDAAPG-AYYVRPALVRMPAQTAVVREETFAPILYVL 407
            + +   R   E   +   GE     A  G   +  P    +P    + R E F P+L+V+
Sbjct: 913  LVDHAARMDQEAKKI---GEVALDPATTGNGTFFAPRAYEIPGLATLTR-EIFGPVLHVI 968

Query: 408  TYR--DLDEAIRLNNEVPQACRQG--SRTDG------APADDPRCRARRRAGGANCPAVP 457
             ++  +LD+ +   N        G  SR D       + A    C   R   GA     P
Sbjct: 969  RWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNRNQIGAVVGVQP 1028

Query: 458  ----GRSGTGAGAGG 468
                G SGTG  AGG
Sbjct: 1029 FGGEGLSGTGPKAGG 1043


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: 971
Number of extensions: 36
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: 1074
Length adjustment: 40
Effective length of query: 456
Effective length of database: 1034
Effective search space:   471504
Effective search space used:   471504
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 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