GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Verminephrobacter eiseniae EF01-2

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011809698.1 VEIS_RS09480 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-13361
         (500 letters)



>NCBI__GCF_000015565.1:WP_011809698.1
          Length = 501

 Score =  325 bits (834), Expect = 2e-93
 Identities = 179/466 (38%), Positives = 267/466 (57%), Gaps = 10/466 (2%)

Query: 38  INPVNGKLISDVFEADAKQVNEAVVAAQNAL-KGPWGKLSVQDRAALIHKIADGIQARFE 96
           ++P   +L++   EA A  V +A+ AA+ A  +GPW     ++RA  +H+IA+ I A  E
Sbjct: 31  VDPATERLLTQAAEAGAADVQQAIAAARRAFDEGPWRDSGTRERARWLHRIAEAIAADAE 90

Query: 97  EFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVR 156
                E  +TG+ + ++RT D+    A FR FA L  T+   + E         ++ T+R
Sbjct: 91  HLATLESLNTGKTISESRT-DMGDIAATFRYFAALVATASGRVNEAPPH----VISRTLR 145

Query: 157 KPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPG 216
           +P+GV G+I+PWN PLL   WK+APAL  GNTVV KPSE +P S   LAE++ D G+PPG
Sbjct: 146 EPVGVCGLITPWNYPLLQAAWKLAPALGAGNTVVLKPSELTPLSTHRLAELLIDIGLPPG 205

Query: 217 VFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAV 276
           VFNL+ G G+  AG  L +H  +  L+FTG +  G+ +M A +   K+++ ELGGKN  +
Sbjct: 206 VFNLVTGSGE--AGAELARHREVDLLSFTGGALAGAAVMNAASGNFKKLALELGGKNPNI 263

Query: 277 VFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQ 336
           VF DAD D A++  L ++F ++GQVC    R+ V   I D FV  L     R+ +G    
Sbjct: 264 VFDDADFDTALDYALNAAFFHAGQVCSAGSRLMVQSGIHDRFVDALVARTRRIRLGNGFA 323

Query: 337 DGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVP--KFNDERDQGAYVQPTIWTGL 394
           DG  MGP+ S   R KV++     V++GA +  GG  P  +      +G +++P + T +
Sbjct: 324 DGTQMGPVQSALQRQKVMAMVAAGVEQGAVLRCGGKAPAAQAGQTFGRGFWLEPAVLTNV 383

Query: 395 SDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVG 454
             +    TEEIFGPV  +  F  E E +   N + +GLA A+WT +L RA+RVSR +  G
Sbjct: 384 RAEMALATEEIFGPVLTVERFGSEQEALRHANATPFGLAAAVWTRDLDRANRVSRALRFG 443

Query: 455 LVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500
            VW N ++      P+GG K SG+GRE G   +D Y+++ +  I +
Sbjct: 444 TVWANDYHPYFPEAPWGGYKASGIGRELGPGGLDEYTELKHSYINL 489


Lambda     K      H
   0.318    0.135    0.405 

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: 584
Number of extensions: 22
Number of successful extensions: 4
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: 500
Length of database: 501
Length adjustment: 34
Effective length of query: 466
Effective length of database: 467
Effective search space:   217622
Effective search space used:   217622
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 (21.7 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