GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Desulfacinum infernum DSM 9756

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_084076256.1 BUB04_RS06460 aspartate aminotransferase family protein

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_900129305.1:WP_084076256.1
          Length = 449

 Score =  274 bits (700), Expect = 5e-78
 Identities = 157/434 (36%), Positives = 241/434 (55%), Gaps = 15/434 (3%)

Query: 21  HLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATR 80
           H+     Y+ L +K   ++ + EGVYIWD  G + +D   G   V++G+G  E+++A   
Sbjct: 5   HMKDHIFYRNL-KKTYPVVDRGEGVYIWDKNGKRYIDGSGGACVVSIGHGVPEILEAMKE 63

Query: 81  QMRELPFYNLFFQTAHPPVVELAKAIADVAPE-GMNHVFFTGSGSEANDTVLRMVRHYWA 139
           Q R + F +    T+    +E A+ +  +AP+  +N V+F   GSEA +T +++VR YW 
Sbjct: 64  QARRICFAHGSHFTSEA-ALECAERLVRMAPDPALNRVYFLSGGSEAVETAVKVVRQYWR 122

Query: 140 TKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMS 199
             G+P K  VI RW  +HG+T   ++LGG     +          HI   Y Y       
Sbjct: 123 EVGKPDKYKVISRWTSFHGNTTGALALGGHTGRRKHYHPLFLHTPHIEPAYCYRCPFGRE 182

Query: 200 PDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGA-GGVIVPPDTYWPKIREILAKYDIL 258
           P+   +  A+QLE+ I   G + VAAFIAEP+ GA  G +VP D YW +IREI   Y + 
Sbjct: 183 PEACSLECADQLERTIKYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICNAYQVK 242

Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG-G 317
            IADEV+ G GRTG+ F   ++   PD++  AKGL+SGY P+G V+V++EI + +  G G
Sbjct: 243 LIADEVMTGVGRTGQNFCLDHWKVVPDVIVTAKGLSSGYTPLGAVIVKEEIHDAIRSGSG 302

Query: 318 EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARG 377
            F HG TY  +P++AA+    +R L E+ ++ +        L ++ Q L +HP VG+ RG
Sbjct: 303 AFVHGHTYCQNPLSAAIGAAVLRYLEEQNLVAR-SERMGKVLLEKLQVLLEHPTVGDVRG 361

Query: 378 VGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIM--------RAVGDTMIISPP 428
           +G+ A +ELV++KKT+  F     +     +  FR GLI            GD ++++PP
Sbjct: 362 LGLFAGVELVRDKKTKATFDPSLKINARVAQEAFRRGLITYPGSGGADGIHGDHILLAPP 421

Query: 429 LVIDPSQIDELITL 442
            VI  SQID+L+ +
Sbjct: 422 FVITESQIDDLVRI 435


Lambda     K      H
   0.320    0.138    0.425 

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: 588
Number of extensions: 32
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: 456
Length of database: 449
Length adjustment: 33
Effective length of query: 423
Effective length of database: 416
Effective search space:   175968
Effective search space used:   175968
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: 51 (24.3 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