GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sphingobium czechense LL01

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::pseudo5_N2C3_1:AO356_13150
         (454 letters)



>NCBI__GCF_001046645.1:WP_066609126.1
          Length = 462

 Score =  345 bits (885), Expect = 2e-99
 Identities = 185/442 (41%), Positives = 268/442 (60%), Gaps = 13/442 (2%)

Query: 14  LSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELA 73
           +  DH + P + F+  +  G  ++   KG++L D EG +++D  AGLWCV VGYG++ +A
Sbjct: 12  IDRDHLIHPVTSFRGHEAHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIA 71

Query: 74  DAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVR 133
           +AA++QMR LPY   +F     P ++L++ + D++PEG++HV+FT  GS+  D+ +R + 
Sbjct: 72  EAAAEQMRRLPYATGYFHFGSEPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYIT 131

Query: 134 HYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEG 193
           HY    G+P KK  I+ + GYHGS+  GA L  +   H   DLP+    HIA PY +   
Sbjct: 132 HYHNAIGKPEKKQFIALERGYHGSSSTGAGLTALANFHRGFDLPLRWQHHIASPYPY--R 189

Query: 194 GDMSPEEFGVWA--ANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILA 251
            D+  ++  + A    +L++K+ ++G DNV AF  EPIQG+GGVIVPP  +   M+E   
Sbjct: 190 SDLEGDDAAIIARSVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCT 249

Query: 252 KYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVL 311
           + DILFV DEVI GFGRTG  F  +  G+ P +MT+AKGLT+GY+PMG L++   V   +
Sbjct: 250 QLDILFVTDEVITGFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGI 309

Query: 312 NEGG----DFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKRLRELNDH 367
             G        HG TYSGHPV+AAV LE +R+  D  I+       A      L  L +H
Sbjct: 310 ANGAAPEVAIGHGATYSGHPVSAAVGLEVLRLYTDGGILAN-GQRVATRFDAGLAGLANH 368

Query: 368 PLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQF--CFDNGLIMRAVGDTMI-IA 424
           P+VG+ RG GLLGAIELV DK ++ R++  G+ +  R F   +DNG+I RA  D +I +A
Sbjct: 369 PMVGDTRGRGLLGAIELVADKGSKARFD-PGLKLADRLFAKAYDNGVIFRAFADNIIGLA 427

Query: 425 PPLVISKAEIDELVTKARHCLD 446
           P L  S  E+DE+  +    LD
Sbjct: 428 PALCASDGEMDEIFARIAKTLD 449


Lambda     K      H
   0.320    0.139    0.431 

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: 593
Number of extensions: 23
Number of successful extensions: 6
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: 454
Length of database: 462
Length adjustment: 33
Effective length of query: 421
Effective length of database: 429
Effective search space:   180609
Effective search space used:   180609
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