GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Leeuwenhoekiella blandensis MED217

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_009778838.1 MED217_RS02180 aldehyde dehydrogenase (NADP(+))

Query= reanno::pseudo6_N2E2:Pf6N2E2_612
         (526 letters)



>NCBI__GCF_000152985.1:WP_009778838.1
          Length = 525

 Score =  484 bits (1247), Expect = e-141
 Identities = 259/520 (49%), Positives = 335/520 (64%), Gaps = 5/520 (0%)

Query: 4   ILGHNYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYRSLS 63
           I G NYIG   SA G+T   +++          F +AT  EVDAAA+ AA A+  Y+  S
Sbjct: 2   ITGKNYIGSKISAEGKTTYTTINPKLNIENEWQFTEATESEVDAAAQLAAEAFEVYKHKS 61

Query: 64  AVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRRGDF 123
              RA FL AI +E++ALG + +     E+ LP  R  GERGRT GQ+  FA +L +GD+
Sbjct: 62  DKERAAFLRAIGEEIEALGQQLIDTYTTESGLPEGRAMGERGRTIGQLNAFASLLEQGDW 121

Query: 124 YGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGCPVV 183
             A ID   PERTP P+PDLR+ +I  GPVAVFGASNFP AFSTAGGDTASALAAGCPVV
Sbjct: 122 VQATIDHGNPERTPAPKPDLRKMQIATGPVAVFGASNFPFAFSTAGGDTASALAAGCPVV 181

Query: 184 FKAHSGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGG--VGEWLVKHPAIQAVGFTGS 241
            K+H  H AT E V+ AII+AA+KT MP GVF+ +   G  VGE LVKHPAI+ VGFTGS
Sbjct: 182 VKSHPMHAATGELVSSAIIKAAQKTGMPDGVFSNLNSKGIAVGEQLVKHPAIKGVGFTGS 241

Query: 242 LKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQFC 301
           +K G+AL  + A R +PIPV+AEM SINPV++LP+AL+   ES A+    S+  G GQFC
Sbjct: 242 IKAGKALVALGANREEPIPVYAEMGSINPVVILPEALKVNGESWAQKYAGSINLGAGQFC 301

Query: 302 TNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLAG 361
           TNPGL++GI   +   F + +A  +G+Q    ML+     +Y  G Q +L   G E LA 
Sbjct: 302 TNPGLILGIEGEELETFGKNLATHLGEQPAHCMLHPNIQSAYESGKQTMLDAAGTEVLAV 361

Query: 362 --RQQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQL 419
               +  N  +P L K      +  +  L  EVFGP ++ V    +AQL   LN L GQL
Sbjct: 362 TLEAEGANDGKPALVKVTGDNFL-ANTKLHAEVFGPFSMLVSCTSKAQLLEVLNALEGQL 420

Query: 420 TATMIGEPADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSV 479
           T ++I E ++   ++++   L  +VGRIL NG PTGVEVC +M HGGP+P++SDA+ TSV
Sbjct: 421 TGSLIAETSEVATYTDVIDALRSRVGRILFNGVPTGVEVCPAMHHGGPFPSSSDAKFTSV 480

Query: 480 GTLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDG 519
           G  AI R++RPV +Q++P  LLP+ LK  NPLGILR VDG
Sbjct: 481 GNDAIYRWVRPVSYQDWPQELLPDALKEENPLGILRKVDG 520


Lambda     K      H
   0.319    0.135    0.395 

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: 698
Number of extensions: 29
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: 526
Length of database: 525
Length adjustment: 35
Effective length of query: 491
Effective length of database: 490
Effective search space:   240590
Effective search space used:   240590
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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