Alignments for a candidate for glnA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Echinicola vietnamensis KMM 6221, DSM 17526

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Echvi_2357 Echvi_2357 Uncharacterized protein related to glutamine synthetase

Query= BRENDA::Q5LGP1
         (729 letters)



>FitnessBrowser__Cola:Echvi_2357
          Length = 711

 Score =  775 bits (2001), Expect = 0.0
 Identities = 393/719 (54%), Positives = 501/719 (69%), Gaps = 11/719 (1%)

Query: 12  LSNRKPLEITTPSNKLSDYYASHVFDRKKMQEYLPKEAYKAVVDATEKGTPISREMADLI 71
           + +R  +    PS+K+SDY+ S VF   KM++ L    YK V +A EKG+ I    A+ +
Sbjct: 3   VQSRGNVPFEAPSSKISDYFGSEVFGLSKMKDALAPSVYKKVSEAIEKGSKIDTSSAEEV 62

Query: 72  ANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGEVIERFSGKLLIQQEPDAS 131
           A   K+WA S  VTHYTHWFQPLT  TAEKHD F +       IERF G  L+QQEPDAS
Sbjct: 63  ATAAKAWALSKGVTHYTHWFQPLTGSTAEKHDTFFDAHAK---IERFKGSALVQQEPDAS 119

Query: 132 SFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYKTPLLKALAAVD 191
           SFPNGGIR TFEARGYTAWD SSP F+ + TLCIPTIF+SYTGEALDYKTPLLK++ AV 
Sbjct: 120 SFPNGGIRTTFEARGYTAWDPSSPMFIFENTLCIPTIFVSYTGEALDYKTPLLKSVEAVS 179

Query: 192 KAATEVCQLFDKNITRVFTNLGWEQEYFLVDTSLYNARPDLRLTGRTLMGHSSAKDQQLE 251
            AAT +CQLFD+++ +V  +LG EQEYF++D +LY +RPDL + GRT+ GH+ A+ QQL+
Sbjct: 180 AAATPICQLFDRSVKKVNPSLGVEQEYFVIDKALYASRPDLVMAGRTVFGHNPARGQQLD 239

Query: 252 DHYFGSIPPRVTAFMKELEIECHKLGIPVKTRHNEVAPNQFELAPIFENCNLANDHNQLV 311
           DHYFGSIP RV AFMK  EIE  KLGIPV TRHNEVAP QFE+AP+FE  N A DHNQL+
Sbjct: 240 DHYFGSIPGRVKAFMKHFEIEALKLGIPVSTRHNEVAPGQFEVAPVFEEINKATDHNQLL 299

Query: 312 MDLMKRIARKHHFAVLFHEKPYNGVNGSGKHNNWSLCTDTGINLFAPGKNPKGNMLFLTF 371
           MDLM ++A +HH  VLFHEKP+ G+NGSGKHNNWSL TDTG+NLF P  + + N+ FLTF
Sbjct: 300 MDLMDKVADQHHLKVLFHEKPFAGLNGSGKHNNWSLITDTGVNLFQPSNSARENLQFLTF 359

Query: 372 LVNVLMMVHKNQDLLRASIMSAGNSHRLGANEAPPAILSIFLGSQLSATLDEIVRQVTNS 431
           LV  +  VH + D+LRASI SAGN  RLGANEAPPAI+S+FLGS L+A LDE+ +   N 
Sbjct: 360 LVATVKAVHDHADILRASIASAGNDFRLGANEAPPAIISVFLGSTLTAVLDELEKN-GNI 418

Query: 432 KMTPEEKTTLKLGIGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSSANCAAAMIAINA 491
           K+   +   +KLGI +IPEI+LD TDRNRTSPFAFTGN+FEFRA GSS+N A  M A+N 
Sbjct: 419 KIEKGDNMYMKLGISKIPEIILDNTDRNRTSPFAFTGNKFEFRAVGSSSNVAGPMTALNV 478

Query: 492 AMANQLNEFKASVDKLMEEGIGKDEAIFRILKENIIASEPIRFEGDGYSEEWKQEAARRG 551
             A+ L      +   +E G  K  AI  +L++ I  S+ +RFEGDGYSEEW++EA +RG
Sbjct: 479 IAADTLKLMYKDIQAEIEGGKEKKIAIVNVLRKYIKESKKVRFEGDGYSEEWEKEAEKRG 538

Query: 552 LTNICHVPEALMHYMDNQSRAVLIGERIFNETELACRLEVELEKYTMKVQIESRVLGDLA 611
           L+N+   P AL   +   +  +     + N TEL  R E+ LE Y MKVQIESRV+GDLA
Sbjct: 539 LSNLKSTPFALDVLVAKATSELYEKHNVMNITELHARHEIRLENYIMKVQIESRVMGDLA 598

Query: 612 INHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKEISHRVSAIKVLVRDMT 671
           +NH++P A+ YQ +L+EN   +K +  + +  +      + I EIS  + AIK  V  M 
Sbjct: 599 LNHVIPTAIQYQTKLIENANGLKSLGLDSKAAI------DTINEISKHIEAIKENVSAMI 652

Query: 672 EARKVANHKENFKEKAFAYEETVR-PYLESIRDHIDHLEMEIDDEIWPLPKYRELLFTK 729
           +AR+  N +E+  ++A  Y   V+  + E IR  +D LE+ +DDE WPL KYRE+LF +
Sbjct: 653 DARRRLNKEEDIAKRAKGYSTDVKDAFFEKIRYSVDKLELFVDDEFWPLVKYREMLFLR 711


Lambda     K      H
   0.319    0.134    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: 1249
Number of extensions: 48
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: 729
Length of database: 711
Length adjustment: 40
Effective length of query: 689
Effective length of database: 671
Effective search space:   462319
Effective search space used:   462319
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 (21.7 bits)
S2: 55 (25.8 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis