GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Amycolatopsis halophila YIM 93223

Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= SwissProt::D4GP41
         (482 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  332 bits (851), Expect = 2e-95
 Identities = 192/479 (40%), Positives = 269/479 (56%), Gaps = 9/479 (1%)

Query: 8   YVNGEWV-TSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDE--WRNTPG 64
           +++G WV T+ T     V NPAN +E+    + ++E D  AAV AA  A D+  WR T  
Sbjct: 5   FIDGRWVDTTGTAPARVVLNPANAAELATVCE-ADEKDVDAAVAAARRAFDDSPWRATTA 63

Query: 65  PERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGT 124
            ERG +LRE   LL + K+ L    + + GK   E   +V     +F Y+++ A +  G 
Sbjct: 64  RERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGR 123

Query: 125 KKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVV 184
                  +       EPVGV +LI PWNYP+   +WKLAPALAAGNTVV+KP+ + P   
Sbjct: 124 VVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTT 183

Query: 185 IEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAG 244
           IE+ R ++EAG+P GV+N+V G G++VG+  + +   DLVSFTG  + G+ +   A +  
Sbjct: 184 IELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGV 243

Query: 245 KRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAEL 304
           KRV  ELGGKNP +V   A+   A D      F  +GQ C+A SR IV  D++D+FVAEL
Sbjct: 244 KRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAEL 303

Query: 305 VDRAESLDVGPGTD--HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362
             RA+++ +G G D   E GP  S         +I+ A+ EGA LV GG  P    +  G
Sbjct: 304 ARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELADG 363

Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422
           +F+ PTVF D D +MRI Q+EVFGPVV V      DE + +AND +YGL+ ++ T D + 
Sbjct: 364 YFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDASR 423

Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVYDS 481
           A R    +  G V +ND    L     +GGF +S     RE G +GL+ Y   K +Y +
Sbjct: 424 AQRVAGALRHGTVWINDFHPYLP-QAEWGGFGKSG--IGRELGPSGLEEYRETKHIYQN 479


Lambda     K      H
   0.310    0.130    0.370 

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: 612
Number of extensions: 31
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: 482
Length of database: 496
Length adjustment: 34
Effective length of query: 448
Effective length of database: 462
Effective search space:   206976
Effective search space used:   206976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 52 (24.6 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