GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Desulfitobacterium hafniense DCB-2

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_015945221.1 DHAF_RS22210 aminodeoxychorismate synthase, component I

Query= curated2:Q9X6J4
         (508 letters)



>NCBI__GCF_000021925.1:WP_015945221.1
          Length = 721

 Score =  283 bits (725), Expect = 1e-80
 Identities = 179/508 (35%), Positives = 272/508 (53%), Gaps = 47/508 (9%)

Query: 26  LADVIEPLQVFANLRE-EAVFLLESKDDESPWARYSFIGVAPFLTLESETGETFLIK--- 81
           LA  ++P+++    +E E  F L+S  +     RYSF+G  PFL   S   +   +K   
Sbjct: 209 LAIDLQPIELLEAFKESEYPFFLDSGRNYGGLGRYSFMGAFPFLQA-SACRDGVEVKRFA 267

Query: 82  -DENGNVQMTASTLKEAFQAVERALCVKPLAEAA-----------PFTGGAVGFLGYDFI 129
            +E G+ +  +S + + + A      +K L +             PF GGAVGF  YD  
Sbjct: 268 GEEEGSKEDLSSLIGQEWLAYPEGESLKILDDLVERYRVPNPTEFPFVGGAVGFWTYDLK 327

Query: 130 SAIEKVPRHRAPDLAMKAGHFVFCESLFAFDHEKRELSLIHYIRLKGHETMQEKIAIYRA 189
             +EK+P+    DL +    F + + +  +DHE R  +L+     +  E  +   A+ +A
Sbjct: 328 DELEKMPQSGINDLDLPLWRFSWYDGIVVYDHENRRYTLLACGMTESGECRR---ALAQA 384

Query: 190 AEERIAAL--------AAKASRP---RAEQPLLPAE--DEAERAALF------------- 223
             ER+  +          K   P    A Q  + A    + ER+  +             
Sbjct: 385 RVERLVGVLEGFLEGRGGKGDHPGTAAAYQRQIGARIGTQQERSGTYQGHDESQDMEQPQ 444

Query: 224 SKASSNYEKEQFLRDVEAVKQYIAAGDVFQAVLSQRFSVPVQAGGFAIYRILRHINPSPY 283
            +      KEQ+L D++ V  YI AGD++QA L+QRF  P      A+Y+ L   NP+P+
Sbjct: 445 ERVHYTVSKEQYLLDLQRVIDYIYAGDIYQANLTQRFQFPYTKEPMALYKALHAHNPAPF 504

Query: 284 MFYFRLDGIEIVGSSPEKLIQVRNR-RAEIDPIAGTRRRGRSPAEDEKLADELYHDPKER 342
             +   +  +I+ SSPE+ +Q+  +   E  PI GTR RG++P EDE  A EL    K+R
Sbjct: 505 AAFLPYEDFQILSSSPERFVQISAQGEIETRPIKGTRPRGKTPEEDEAYARELTESTKDR 564

Query: 343 AEHYMLVDLARNDIGRVAKYGTVEVPVLMEIGKFSHVMHLISKVVGVLDDDIHPIDALLA 402
           AE  M++DL RND+GR+ +YG+V V  L+ + ++  V HL+S +VG L  ++   + L A
Sbjct: 565 AELTMIIDLQRNDLGRICRYGSVRVTDLIRLEQYPTVWHLVSTIVGKLKPELKTSEILKA 624

Query: 403 AFPAGTVSGAPKVRAMQILQELEPTARGLYAGAIAYIGFDGSIDSCIAIRTAVIKDGYAY 462
            FP G+++GAPK+RAM+I++ELEP  RGLY G+I Y+GFDG+ D+ I IRT ++KDG AY
Sbjct: 625 IFPGGSITGAPKIRAMEIIEELEPYKRGLYTGSIGYMGFDGAWDTNIVIRTILLKDGQAY 684

Query: 463 VQAGAGIVADSVPELEWKETRNKASALI 490
              G GIVADSVPE E++E   K  AL+
Sbjct: 685 FNGGGGIVADSVPEEEYQEALQKVKALL 712


Lambda     K      H
   0.321    0.137    0.390 

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: 814
Number of extensions: 28
Number of successful extensions: 4
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: 508
Length of database: 721
Length adjustment: 37
Effective length of query: 471
Effective length of database: 684
Effective search space:   322164
Effective search space used:   322164
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 (21.9 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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