GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Klebsiella michiganensis M5al

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= CharProtDB::CH_002469
         (406 letters)



>FitnessBrowser__Koxy:BWI76_RS11670
          Length = 406

 Score =  687 bits (1772), Expect = 0.0
 Identities = 335/406 (82%), Positives = 365/406 (89%)

Query: 1   MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL 60
           MSQ ITR NFDEWM+PVYAPA FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHP L
Sbjct: 1   MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60

Query: 61  REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA 120
            +AL EQA KFWHTGNGYTNEPVLRLAK+LIDATFADRVFFCNSGAEANEAALKLARK+A
Sbjct: 61  VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120

Query: 121 HDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALI 180
           HDR+GS KSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLP  I+HA YND++SA ALI
Sbjct: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180

Query: 181 DDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240
           DD+TCAVIVEP+QGEGGVVPA   FL+GLRELC+ HNALLIFDEVQTGVGRTGELYAYMH
Sbjct: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240

Query: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300
           YGVTPDLL+TAKALGGGFP+GALLA+E CA VMTVGTHGTTYGGNPLA AVAG+V   IN
Sbjct: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300

Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK 360
           T E+LNGVKQRH WF ERLN IN RYGLF E+RGLGLLIGCVL  +YAG+AK IS +AA+
Sbjct: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360

Query: 361 AGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEHFVSRGSS 406
            G+M+LIAG NVVRFAPAL +SE+EV +GLDRF  AC+ F++  SS
Sbjct: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406


Lambda     K      H
   0.319    0.136    0.407 

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: 623
Number of extensions: 20
Number of successful extensions: 1
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: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 Aug 03 2021. The underlying query database was built on Aug 03 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