GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sinorhizobium fredii NGR234

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000018545.1:WP_012708832.1
          Length = 502

 Score =  306 bits (783), Expect = 1e-87
 Identities = 177/484 (36%), Positives = 263/484 (54%), Gaps = 23/484 (4%)

Query: 9   GELVSGEGEKQPVYN-------PATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPK 61
           G  + GE  ++PV         P TG  L +IA + A  ++ A+ AA AA  +WG+T+  
Sbjct: 16  GNFIGGEW-REPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAAKEKWGRTSTT 74

Query: 62  VRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL 121
            R+  L+K+A  +E+N ++ A  E+ + GKP+      +IP  +D FR+FA   R   G 
Sbjct: 75  ERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQEG- 133

Query: 122 AAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTA 181
           + GE      +    +PLGVV  I PWN+P++MAAWK+APALAAGNCVVLKP+E TP + 
Sbjct: 134 SIGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQTPASI 193

Query: 182 LKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIK 241
           L LAEL  D+ P GV+NI+ G G   G PL   P++  ++ TG   TG  I+ + + ++ 
Sbjct: 194 LILAELIADLLPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYASQNLI 253

Query: 242 RTHMELGGKAPVIVF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDT 295
              +ELGGK+P I F      DD   +  +EG   F   N G+ CT   R   Q+ IYD 
Sbjct: 254 PVTLELGGKSPNIFFADVLNEDDDYFDKALEGFAMFA-LNQGEVCTCPSRALVQESIYDR 312

Query: 296 LVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG----- 350
            +E+    V  ++ G P D +T +G  +S   LE++   ++  K  G  +V+ GG     
Sbjct: 313 FMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEG-AEVLAGGGRNVL 371

Query: 351 EKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSV 410
           E     GYY  PT+  G      I Q+E+FGPVVSVT F  E++ +  AND+ YGL + V
Sbjct: 372 EGDLAGGYYVKPTVFRGH-NKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTLYGLGAGV 430

Query: 411 WTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470
           W++D  R +R    +Q G  W N +    +    GG K SG G++     L+ Y   +++
Sbjct: 431 WSRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 490

Query: 471 MVKH 474
           +V +
Sbjct: 491 LVSY 494


Lambda     K      H
   0.317    0.134    0.397 

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: 603
Number of extensions: 27
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: 474
Length of database: 502
Length adjustment: 34
Effective length of query: 440
Effective length of database: 468
Effective search space:   205920
Effective search space used:   205920
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 Apr 09 2024. 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