GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Phaeobacter inhibens BS107

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate GFF1439 PGA1_c14560 homoserine O-succinyltransferase MetA

Query= SwissProt::Q5LSN6
         (312 letters)



>FitnessBrowser__Phaeo:GFF1439
          Length = 305

 Score =  553 bits (1426), Expect = e-162
 Identities = 254/304 (83%), Positives = 281/304 (92%)

Query: 1   MPIKIPAHLPAYDILTREGVMVMSEDQAARQDIRPLRIGLLNLMPKKIQTETQFARLIGA 60
           MPIKIP+ LPAYD+LT EGVMVMS DQAARQDIRPLRIGLLNLMPKKIQTE QFARLIGA
Sbjct: 1   MPIKIPSDLPAYDVLTNEGVMVMSPDQAARQDIRPLRIGLLNLMPKKIQTENQFARLIGA 60

Query: 61  TPLQIELSLIRMTEHQTKTTASEHMEEFYRPFQEVRDEKFDGLIITGAPIEHLEFSDVTY 120
           TPLQI+LSLIRMTEHQT+ TA+EHM EFYRPFQE++D++FDGLIITGAPIEHLEF DVTY
Sbjct: 61  TPLQIDLSLIRMTEHQTRNTAAEHMAEFYRPFQEIKDQRFDGLIITGAPIEHLEFEDVTY 120

Query: 121 WDELGEVFAWTQSNVHSTFGVCWGGMAMINHFHGIRKHMLDHKAFGCFRHRNLDPASPYL 180
           WDEL EVF WTQ+NVHSTFGVCWGGMAMIN+FHG++KH+LDHK FGCFRH+NLDPASPYL
Sbjct: 121 WDELCEVFDWTQTNVHSTFGVCWGGMAMINYFHGVKKHLLDHKVFGCFRHQNLDPASPYL 180

Query: 181 RGFSDDFVIPVSRWTEVKQAEVDAVPELVTLLGSDEVGPCLISDPGHRALYIFNHFEYDS 240
           RGFSDD VIPVSRWTE++Q+E+DA P L +LLGS + GPCLI DP HRALYIFNHFEYDS
Sbjct: 181 RGFSDDCVIPVSRWTEIRQSEIDARPGLRSLLGSQDAGPCLIEDPSHRALYIFNHFEYDS 240

Query: 241 DTLKQEYDRDVEGGTAINVPINYYPDDDPSRKPLNRWRSHAHLLYGNWISEIYETTPYDM 300
           DTLKQEYDRDV  GT INVP+NYYPDDDPSRKP NRWRSHAHLLYGNWI++IY++TP+DM
Sbjct: 241 DTLKQEYDRDVASGTPINVPMNYYPDDDPSRKPQNRWRSHAHLLYGNWINDIYQSTPFDM 300

Query: 301 ARIG 304
           A IG
Sbjct: 301 AEIG 304


Lambda     K      H
   0.321    0.139    0.433 

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: 483
Number of extensions: 7
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: 312
Length of database: 305
Length adjustment: 27
Effective length of query: 285
Effective length of database: 278
Effective search space:    79230
Effective search space used:    79230
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: 48 (23.1 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