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_110206407.1 DNK54_RS08025 succinate-semialdehyde dehydrogenase (NADP(+))

Query= SwissProt::P9WNX7
         (518 letters)



>NCBI__GCF_003194585.1:WP_110206407.1
          Length = 538

 Score =  437 bits (1125), Expect = e-127
 Identities = 230/483 (47%), Positives = 308/483 (63%), Gaps = 1/483 (0%)

Query: 35  GKPLTTIPVGTAADVEAAFAEARAAQTDWAKRPVIERAAVIRRYRDLVIENREFLMDLLQ 94
           G+PL  IP  +  DV AAF  AR AQ  W++  +  RA ++ R   LV++  E + D+  
Sbjct: 56  GQPLAVIPQSSDDDVRAAFERARRAQAAWSRTSLDHRAEIMLRLHKLVLDRAEEICDVAV 115

Query: 95  AEAGKARWAAQEEIVDLIANANYYARVCVDLLKPRKAQPLLPGIGKTTVCYQPKGVVGVI 154
            E+GKAR  A  E   +   A YYAR     +  ++   ++P   +  V   PKGVVG+I
Sbjct: 116 WESGKARKDAYLEAYHVALTARYYARTIHRHMDSQRRPGVVPLATRIDVNRVPKGVVGII 175

Query: 155 SPWNYPMTLTVSDSVPALVAGNAVVLKPDSQTPYCALACAELLYRAGLPRALYAIVPGPG 214
           SPWNYP T+ + D +PAL+AGNAVV KPDSQT   AL  A+LL  AG P+ L+ +V GPG
Sbjct: 176 SPWNYPFTMALCDGLPALMAGNAVVAKPDSQTMLTALLGAQLLEEAGFPKDLWTVVAGPG 235

Query: 215 SVVGTAITDNCDYLMFTGSSATGSRLAEHAGRRLIGFSAELGGKNPMIVARGANLDKVAK 274
           S VGT I +N DY+ FTGS+ATG R+A     RLIG S ELGGKNP+++ R A+++  A+
Sbjct: 236 SRVGTRIIENADYVCFTGSTATGKRVAAGCAERLIGCSLELGGKNPILILRDADIETAAE 295

Query: 275 AATRACFSNAGQLCISIERIYVEKDIAEEFTRKFGDAVRNMKLGTAYDFSVDMGSLISEA 334
            ATRA FSNAGQLC+S ER+ V  +I + F  +F      M LG  +++  DMGSLIS+ 
Sbjct: 296 GATRATFSNAGQLCVSTERMMVADEIYDRFVERFVARTEAMVLGPGHNWETDMGSLISQD 355

Query: 335 QLKTVSGHVDDATAKGAKVIAGGKARPDIGPLFYEPTVLTNVAPEMECAANETFGPVVSI 394
           QL TV  HV DA AKGAKV+ GGK RPD+GP F+EPT+L  V  EM C  NETFGPV+S+
Sbjct: 356 QLDTVKAHVADAVAKGAKVLTGGKHRPDLGPFFFEPTILEGVTEEMTCFGNETFGPVISL 415

Query: 395 YPVADVDEAVEKANDTDYGLNASVWAGSTAEGQRIAARLRSGTVNVDEGYAFAWGSLSAP 454
           Y   D  +A+ KAN+ +YGLNAS+++      + IA  ++ GTVN++EGY   + SL AP
Sbjct: 416 YRFHDETKAIAKANEGNYGLNASIYSRDGKRARAIAREIKCGTVNINEGYGATFASLDAP 475

Query: 455 MGGMGLSGVGRRHGPEGLLKYTESQTIATARVFNLDPPFGIPATVWQKSLLPIVRTVMKL 514
           MGGM  SG+GRR G EG+ +YTE+Q + T R +   P  G+    + K +L +   +MK 
Sbjct: 476 MGGMRESGMGRRQGAEGIHRYTETQAVGTQRGWGFRPVPGMSNETFAK-VLTLNERLMKK 534

Query: 515 PGR 517
            GR
Sbjct: 535 LGR 537


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: 659
Number of extensions: 24
Number of successful extensions: 2
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: 538
Length adjustment: 35
Effective length of query: 483
Effective length of database: 503
Effective search space:   242949
Effective search space used:   242949
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