GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Sphingobium czechense LL01

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_001046645.1:WP_066609126.1
          Length = 462

 Score =  333 bits (853), Expect = 9e-96
 Identities = 179/442 (40%), Positives = 265/442 (59%), Gaps = 13/442 (2%)

Query: 16  LSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELV 75
           + RDH + P T ++     GA ++   +G+++ D EG +++DA AGLWCVNVGYG++ + 
Sbjct: 12  IDRDHLIHPVTSFRGHEAHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIA 71

Query: 76  QAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVR 135
           +AA  QMR LP+   +F     P V+LA+ + D++PEG++HV+FT  GS+A D+ +R + 
Sbjct: 72  EAAAEQMRRLPYATGYFHFGSEPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYIT 131

Query: 136 HYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG 195
           HY    G+P+KK  I    GYHGS+  G  L  +   H   D P+    HIA PY Y   
Sbjct: 132 HYHNAIGKPEKKQFIALERGYHGSSSTGAGLTALANFHRGFDLPLRWQHHIASPYPY--R 189

Query: 196 GDMSPDEFGVWA--AEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILA 253
            D+  D+  + A   ++L+ K+ ++G +NVAAF  EPIQG+GGVIVPP  +   +RE   
Sbjct: 190 SDLEGDDAAIIARSVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCT 249

Query: 254 KYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL 313
           + DILF+ DEVI GFGRTG  F  +  G  PDLM +AKGLT+GY+PMG +++  ++ E +
Sbjct: 250 QLDILFVTDEVITGFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGI 309

Query: 314 NQGG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADH 369
             G        HG TYSGHPV+AAV LE +R+  +  I+   +   A         LA+H
Sbjct: 310 ANGAAPEVAIGHGATYSGHPVSAAVGLEVLRLYTDGGILANGQ-RVATRFDAGLAGLANH 368

Query: 370 PLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCR--EHCFRNGLIMRAVGDTMI-IS 426
           P+VG+ RG G++ A+ELV +K ++ RF D G+ +  R     + NG+I RA  D +I ++
Sbjct: 369 PMVGDTRGRGLLGAIELVADKGSKARF-DPGLKLADRLFAKAYDNGVIFRAFADNIIGLA 427

Query: 427 PPLVIDPSQIDELITLARKCLD 448
           P L     ++DE+     K LD
Sbjct: 428 PALCASDGEMDEIFARIAKTLD 449


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: 566
Number of extensions: 23
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: 456
Length of database: 462
Length adjustment: 33
Effective length of query: 423
Effective length of database: 429
Effective search space:   181467
Effective search space used:   181467
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 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