GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Marinobacter adhaerens HP15

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__Marino:GFF3766
          Length = 425

 Score =  215 bits (547), Expect = 2e-60
 Identities = 136/388 (35%), Positives = 204/388 (52%), Gaps = 34/388 (8%)

Query: 34  SRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHV-SNVFTNEPALRLAHK 92
           + +WD  G+ +IDFAGGI V  +GH HP +V A+  Q +KL H    V   E  ++LA K
Sbjct: 32  AELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVKLAEK 91

Query: 93  L---VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFTV 149
           L   V      +V   NSGAEA E A K+AR        T K  ++     +HGRT +T+
Sbjct: 92  LSGVVPVRGHAKVMLANSGAEALENAMKIARAA------TGKTNVICFDGGYHGRTFYTM 145

Query: 150 NVGGQSK-YSDGFGPKITGITHVPY----------NDLAALKAAV-----SDKTCAVVLE 193
            + G++  Y   FGP    +   PY            L  LK A+     +  T A+V+E
Sbjct: 146 AMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIE 205

Query: 194 PIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTS 253
           P+ GEGG   A  S+L+  R++CD ++ L++ DEVQ+G GR+GK+FA +H GV PD++T 
Sbjct: 206 PVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTM 265

Query: 254 AKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNA 313
           AKS+  G PI+A++ T+         + G TY G+P ACA A AV DV    ++L    A
Sbjct: 266 AKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQA 325

Query: 314 KHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK------AKDIFNAAEREGLM 367
             +K K R  Q  E++     VR LG +    L ++ + +      A  +   A+ +GL+
Sbjct: 326 LGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLI 385

Query: 368 ILQAG--PDVIRFAPSLVVEDADIDAGL 393
           +L  G   + +RF   + +ED  ++ GL
Sbjct: 386 LLSCGMYGNTLRFLMPVTIEDEVLEEGL 413


Lambda     K      H
   0.320    0.136    0.400 

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: 416
Number of extensions: 23
Number of successful extensions: 5
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: 406
Length of database: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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