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_068170525.1 HTA01S_RS10520 aspartate aminotransferase family protein

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



>NCBI__GCF_001592305.1:WP_068170525.1
          Length = 479

 Score =  571 bits (1471), Expect = e-167
 Identities = 281/461 (60%), Positives = 348/461 (75%), Gaps = 6/461 (1%)

Query: 4   QQQDTISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWC 63
           +QQDT  A+QA+D+AH+LHPFTD A LA RG RVI RA+ +Y+WD++G K+LDAM+GLWC
Sbjct: 17  EQQDT-KAIQALDSAHYLHPFTDHAGLASRGARVITRADNIYVWDSEGAKILDAMSGLWC 75

Query: 64  VNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNR----VFFT 119
           VN GYGRK +ADAAY Q+ TLPFYN+FF  T+ PA++LA+K+ASLAP    R    VFF+
Sbjct: 76  VNAGYGRKELADAAYQQMMTLPFYNSFFNTTNVPAVQLATKLASLAPKVGGRSFEHVFFS 135

Query: 120 GSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPI 179
            SGSE+NDTN+RMVRRYWDL G P +K IISR NAYHGST+AGASLGGMG MH QGDLPI
Sbjct: 136 SSGSESNDTNVRMVRRYWDLLGQPQRKVIISRNNAYHGSTMAGASLGGMGGMHAQGDLPI 195

Query: 180 PGIVHIDQPYWFGEGRDMSPEA-FGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVII 238
           P I HI+QPY+F   R    EA FG + A  LEAKILE+G DKVAAFIAEP QGAGGVII
Sbjct: 196 PNITHIEQPYFFENARPGESEADFGRRAAGWLEAKILEVGADKVAAFIAEPVQGAGGVII 255

Query: 239 PPDSYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIP 298
           PP++YW EI+RI+++Y IL I DEVI  FGR G+WFA +  G +PDL+T AKG+TSGYIP
Sbjct: 256 PPETYWPEIQRIVDQYGILLISDEVICAFGRLGHWFAYEKFGYRPDLVTFAKGVTSGYIP 315

Query: 299 MGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPY 358
           +GGV+V DRVA VLI  GGEF HG+TYSGHPVA AVAL N+ ++E E LV +V+ DTGPY
Sbjct: 316 LGGVMVGDRVARVLIEKGGEFNHGYTYSGHPVACAVALANLELMERENLVGRVKDDTGPY 375

Query: 359 LQDRLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMR 418
           L  R   L  HPLVG     G V  + LV +K +   F +++  GM+CR  C ++GL+MR
Sbjct: 376 LARRFAELKDHPLVGGAETCGFVAGLVLVKNKATNAMFDADLGVGMICRGHCFKNGLIMR 435

Query: 419 AVGDTMIISPPLCITRDEIDELIFKASQALSLTLEKIAARG 459
           AVGD MII+PPL +T  +IDE++    + L  TL+ + + G
Sbjct: 436 AVGDRMIIAPPLVMTHAQIDEMMALIVRCLDATLDDLRSAG 476


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: 671
Number of extensions: 23
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 460
Length of database: 479
Length adjustment: 33
Effective length of query: 427
Effective length of database: 446
Effective search space:   190442
Effective search space used:   190442
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