GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Sinorhizobium fredii NGR234

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000018545.1:WP_012708832.1
          Length = 502

 Score =  379 bits (973), Expect = e-109
 Identities = 217/486 (44%), Positives = 288/486 (59%), Gaps = 16/486 (3%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  EW + V+ + F    P TG  +CQ+A  D  D++ A+ AA AA +    W R   +
Sbjct: 18  FIGGEWREPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAAKE---KWGRTSTT 74

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +L ++A  +E +   LA  ET DNGKP   +   D+ + +   RY+A       G 
Sbjct: 75  ERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQEGS 134

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              ID D  +Y  HEP+GV GQIIPWNFP+LM AWK+ PALA GN VV+K AEQTP + L
Sbjct: 135 IGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQTPASIL 194

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +A LI +   PPGV+NIV GFG  AG  +A+   + K+AFTG T  GR+I   A S NL
Sbjct: 195 ILAELIADL-LPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYA-SQNL 252

Query: 280 KRVTLELGGKSPNIIMSDA---DMDWAVEQAH-FALF-FNQGQCCCAGSRTFVQEDIYDE 334
             VTLELGGKSPNI  +D    D D+  +    FA+F  NQG+ C   SR  VQE IYD 
Sbjct: 253 IPVTLELGGKSPNIFFADVLNEDDDYFDKALEGFAMFALNQGEVCTCPSRALVQESIYDR 312

Query: 335 FVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG---IA 391
           F+ER+V R ++   GNP DS T  G Q    Q +KIL YI+ GKQEGA++L GGG   + 
Sbjct: 313 FMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEGAEVLAGGGRNVLE 372

Query: 392 AD--RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVF 449
            D   GY+++PTVF    + M I +EEIFGPV+ +  FKT +E +  AN++ YGL A V+
Sbjct: 373 GDLAGGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTLYGLGAGVW 431

Query: 450 TKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVT 509
           ++D ++     + +QAG VW NCY  + A + FGGYK SG GRE  +  L  Y + K + 
Sbjct: 432 SRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNML 491

Query: 510 VKVPQK 515
           V    K
Sbjct: 492 VSYSPK 497


Lambda     K      H
   0.319    0.136    0.409 

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: 615
Number of extensions: 28
Number of successful extensions: 7
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: 517
Length of database: 502
Length adjustment: 34
Effective length of query: 483
Effective length of database: 468
Effective search space:   226044
Effective search space used:   226044
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 Apr 09 2024. 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