GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_068166979.1 HTA01S_RS02580 aspartate aminotransferase family protein

Query= reanno::SB2B:6938540
         (460 letters)



>NCBI__GCF_001592305.1:WP_068166979.1
          Length = 467

 Score =  332 bits (851), Expect = 2e-95
 Identities = 179/453 (39%), Positives = 268/453 (59%), Gaps = 9/453 (1%)

Query: 9   ISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGY 68
           I+AL A+D AH +HP        KRG  ++  A+G+++ D KG +LLDA AGLWCVNVGY
Sbjct: 10  IAALDALDRAHLIHPVAPWRVHEKRGPNILTGAQGIWLTDGKGQQLLDAFAGLWCVNVGY 69

Query: 69  GRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDT 128
           G++S+  AA  Q++ LP+   +F  + EPAIRLA+K+  ++P  +  V+ T  GSE+ D 
Sbjct: 70  GQESVVQAAAEQMRQLPYATGYFHFSSEPAIRLAAKLVQISPASLQHVYLTLGGSESVDA 129

Query: 129 NLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQP 188
            +R + +Y +  G P KK  I+ +  YHGS+  GA L  +   H+  DLP+P   +I  P
Sbjct: 130 AVRFIVQYHNAIGKPGKKHFIALERGYHGSSSTGAGLTALPVFHRGFDLPLPTQHYIPSP 189

Query: 189 YWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIK 248
             +        +A    +  AL+AK+ ELG + VAAF  EP QG+GGVI+PP  +   ++
Sbjct: 190 NPYRAANPADGQAIIDASVAALKAKVAELGAENVAAFFCEPIQGSGGVIVPPKGWLKAMR 249

Query: 249 RILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRV 308
                 +ILF++DEVI+GFGRTG  FA    G++PDL+T+AKG+TSGY+PMG  ++S++V
Sbjct: 250 EAARALDILFVVDEVITGFGRTGPMFACDAEGVEPDLMTVAKGLTSGYVPMGATLMSNKV 309

Query: 309 ADVLIS---DGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQT 365
              +      G    HG TYS HPV+AAVALE +R+ EE  ++   +     + Q  L  
Sbjct: 310 YSAIADGAPKGAPIGHGATYSAHPVSAAVALEVLRLYEEGGVLANGQRVASAFGQG-LDD 368

Query: 366 LSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425
           L +HPLVG+ R  G++GA+ELV+ K +   F + +           ++G+V RA GD ++
Sbjct: 369 LLSHPLVGDSRHRGLLGALELVSSKSTKAGFDAALDLPNRMAATAYQNGIVFRAFGDNIL 428

Query: 426 -ISPPLCITRDEIDELIFKASQALSLTLEKIAA 457
             +P L  T  +   L+F   + L  TL+ + A
Sbjct: 429 GFAPALTFTESDFG-LMF---ERLKKTLDDVLA 457


Lambda     K      H
   0.321    0.137    0.408 

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: 537
Number of extensions: 17
Number of successful extensions: 3
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: 460
Length of database: 467
Length adjustment: 33
Effective length of query: 427
Effective length of database: 434
Effective search space:   185318
Effective search space used:   185318
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.

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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