GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E3

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AO353_06085 AO353_06085 omega amino acid--pyruvate aminotransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_06085
          Length = 449

 Score =  273 bits (698), Expect = 8e-78
 Identities = 166/457 (36%), Positives = 245/457 (53%), Gaps = 19/457 (4%)

Query: 1   MQQQQQDTISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAG 60
           M   +   +S    +    H  P+T + +  +R  R+I  AEG Y+ D KG K+ D+++G
Sbjct: 1   MNVPENAPVSLASQLKLDAHWMPYTANRNF-QRDPRLIVAAEGSYLIDDKGRKVYDSLSG 59

Query: 61  LWCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTG 120
           LW    G+ RK I +A   QL TL  Y+  FQ  H  + +LA KI  L PG++N VFFT 
Sbjct: 60  LWTCGAGHTRKEIQEAVAKQLGTLD-YSPGFQYGHPLSFQLAEKITELTPGNLNHVFFTD 118

Query: 121 SGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIP 180
           SGSE  DT ++MVR YW LKG  +K  +I R   YHG  +AG SLGG+    +     + 
Sbjct: 119 SGSECADTAVKMVRAYWRLKGQSTKTKMIGRARGYHGVNIAGTSLGGVNGNRKLFGQAMM 178

Query: 181 GIVHIDQPYWFGEGRDMS-PEAFGIKTAQALEAKILELGE-DKVAAFIAEPFQGAGGVII 238
            + H+              P+  GI  A+ L  K++EL +   +AA   EP  G+ GV++
Sbjct: 179 DVDHLPHTLLASNAYSRGMPKEGGIVLAEEL-LKLIELHDASNIAAVFVEPLAGSAGVLV 237

Query: 239 PPDSYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIP 298
           PP  Y   ++ I +++NIL + DEVI+GFGRTG+ F A + G+ PDL+ IAK +T+G IP
Sbjct: 238 PPQGYLKRLREICDQHNILLVFDEVITGFGRTGSMFGADSFGVTPDLMCIAKQVTNGAIP 297

Query: 299 MGGVIVSDRVADVLISDGG-----EFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRT 353
           MG VI S  +    ++        EF HG+TYS HPVA A  L  + +L++E LV  V  
Sbjct: 298 MGAVIASSEIYQTFMNQATPEYAVEFPHGYTYSAHPVACAAGLAALDLLQKENLVQSV-A 356

Query: 354 DTGPYLQDRLQTLSAHPLVGEVRGMGMVGAIELVA-DKHSMVRFGSEISAGMLCREACIE 412
           +  P+ ++ L  L     V ++R  G+ GAI++ A D  ++VR      AGM    A  +
Sbjct: 357 EVAPHFENALHGLKGSKNVIDIRNYGLAGAIQIAARDGDAIVR---PFEAGM----ALWK 409

Query: 413 SGLVMRAVGDTMIISPPLCITRDEIDELIFKASQALS 449
           +G  +R  GDT+   P       ++D L     + L+
Sbjct: 410 AGFYVRFGGDTLQFGPTFNSKPQDLDRLFDAVGEVLN 446


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: 482
Number of extensions: 14
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: 460
Length of database: 449
Length adjustment: 33
Effective length of query: 427
Effective length of database: 416
Effective search space:   177632
Effective search space used:   177632
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 17 2021. 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