GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Nocardioides daejeonensis MJ31

Align Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2; SSADH 2; SSDH 2; EC 1.2.1.79 (characterized)
to candidate WP_110208380.1 DNK54_RS17710 succinate-semialdehyde dehydrogenase (NADP(+))

Query= SwissProt::P9WNX7
         (518 letters)



>NCBI__GCF_003194585.1:WP_110208380.1
          Length = 522

 Score =  420 bits (1079), Expect = e-122
 Identities = 214/456 (46%), Positives = 284/456 (62%)

Query: 26  TRTIDEVFTGKPLTTIPVGTAADVEAAFAEARAAQTDWAKRPVIERAAVIRRYRDLVIEN 85
           T  + EV+TG  L  +P  +  D+EAAFA AR AQ  WA  P+ +R  V +++  LV+E 
Sbjct: 31  TWKLTEVYTGDVLVELPQSSPEDIEAAFAAARRAQKAWAATPLKQRLKVFKKFHSLVLER 90

Query: 86  REFLMDLLQAEAGKARWAAQEEIVDLIANANYYARVCVDLLKPRKAQPLLPGIGKTTVCY 145
            E ++DL+Q E+GKAR  A EE +D+     YY +    +L  RK    +P +  +    
Sbjct: 91  NETIVDLIQVESGKARRMAFEETLDVPMVTGYYLKRAAKVLATRKHAGPVPVVSSSQEVR 150

Query: 146 QPKGVVGVISPWNYPMTLTVSDSVPALVAGNAVVLKPDSQTPYCALACAELLYRAGLPRA 205
            PKGVVG+I+PWN+P    +SD++PAL+AGN VV+KPD++T    L   +LL  AGLP+ 
Sbjct: 151 IPKGVVGIIAPWNFPFATGISDAIPALIAGNGVVVKPDNKTALSPLFGVQLLEEAGLPKG 210

Query: 206 LYAIVPGPGSVVGTAITDNCDYLMFTGSSATGSRLAEHAGRRLIGFSAELGGKNPMIVAR 265
           L+ +V G G  VG  + DN +Y+MFTGS+ TG  + E AGR LIG   ELGGKNPMIV  
Sbjct: 211 LFQVVCGEGPDVGPTLIDNANYVMFTGSTNTGRVIGERAGRNLIGACLELGGKNPMIVLP 270

Query: 266 GANLDKVAKAATRACFSNAGQLCISIERIYVEKDIAEEFTRKFGDAVRNMKLGTAYDFSV 325
            ANLD V K A    F N GQ+C+ IER+YV   I + F  +F +A   + +G AYDF  
Sbjct: 271 DANLDDVVKGALFGAFGNTGQICMHIERMYVHDSIYDTFKARFKEATEKLVVGAAYDFGP 330

Query: 326 DMGSLISEAQLKTVSGHVDDATAKGAKVIAGGKARPDIGPLFYEPTVLTNVAPEMECAAN 385
           ++GSLIS      V+ HV DA  KGA V+ GGK RPD+GP F+EPT+L  V  EM     
Sbjct: 331 NVGSLISVEHKDRVASHVADALEKGATVVTGGKERPDLGPAFFEPTILEGVTEEMLAGVT 390

Query: 386 ETFGPVVSIYPVADVDEAVEKANDTDYGLNASVWAGSTAEGQRIAARLRSGTVNVDEGYA 445
           ETFGPVV+++     DEA+  AN TDYGLNASVW G      R+  R+ SG VN+++  A
Sbjct: 391 ETFGPVVALHRYQTEDEAISLANATDYGLNASVWGGDLDNAIRVGKRIESGNVNINDILA 450

Query: 446 FAWGSLSAPMGGMGLSGVGRRHGPEGLLKYTESQTI 481
            A+ S   P GG+  SGVG RHG +GLLKYT+ Q +
Sbjct: 451 TAYASKGTPSGGVKQSGVGARHGDQGLLKYTDCQNV 486


Lambda     K      H
   0.318    0.134    0.396 

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: 694
Number of extensions: 24
Number of successful extensions: 1
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: 518
Length of database: 522
Length adjustment: 35
Effective length of query: 483
Effective length of database: 487
Effective search space:   235221
Effective search space used:   235221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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