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

GapMind for Amino acid biosynthesis

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

Align glutamine synthetase subunit (EC 6.3.1.2) (characterized)
to candidate WP_005812354.1 DHAF_RS06650 glutamine synthetase

Query= metacyc::MONOMER-13158
         (693 letters)



>NCBI__GCF_000021925.1:WP_005812354.1
          Length = 697

 Score =  822 bits (2124), Expect = 0.0
 Identities = 411/694 (59%), Positives = 512/694 (73%), Gaps = 9/694 (1%)

Query: 6   EIFGSDVFNESVMREKLPKATFKALKKTIDNGDPLAADVANIVANAMKDWAVEKGCTHYT 65
           + FG +VFN++VMRE+LPK T+KAL KTID G PL  +VA +VANAMKDWA+E G THYT
Sbjct: 2   DFFGKNVFNDAVMRERLPKNTYKALHKTIDEGLPLQLEVAEVVANAMKDWAIENGATHYT 61

Query: 66  HWFQPMTGLTAEKLDSFIQPADGGHVIMEFSGKELVKGEPDASSFPSGGLRATFEARGYT 125
           HWFQPMTG TAEK DSFI P   G VIMEFSGKEL+KGEPDASSFP+GG+R+TFEARGYT
Sbjct: 62  HWFQPMTGFTAEKHDSFISPTSDGKVIMEFSGKELIKGEPDASSFPNGGIRSTFEARGYT 121

Query: 126 AWDPTSYAFIKEKT----LCIPTAFCSYNGEALDKKTPLLRSMEAVNRSALRVLKLFGSD 181
           AWD TS AF++E      LCIPTAFCSY GEALDKKTPLLRSME +++ ALR+L+LFG+ 
Sbjct: 122 AWDCTSPAFLREDAGKVILCIPTAFCSYTGEALDKKTPLLRSMETISKQALRILRLFGNT 181

Query: 182 -ATRVISNVGPEQEYFLVDREMYSHRKDLIFTGRTLFGAPAPKGQEMEDHYFGTIKTRVA 240
            A RV   VG EQEYFL++++ +  R DL+ TGRTLFG   PKGQEMEDHYFG I  RV 
Sbjct: 182 TAKRVTPTVGAEQEYFLIEKKYHQKRLDLMLTGRTLFGVLPPKGQEMEDHYFGIINERVT 241

Query: 241 AYMKDLDEQLWKLGIYAKTKHNEVAPAQHELAPIYGTTNIATDHNQLTMEIMKRTARKHG 300
           A+M++++ +LWKLG+ AKT+H E AP Q+E+API+ +TNIATDHNQ+ M+ + + A +HG
Sbjct: 242 AFMQEVNIELWKLGVLAKTQHKEAAPGQYEIAPIFTSTNIATDHNQIIMDTLHKVANRHG 301

Query: 301 FKCLLHEKPFAGINGSGKHNNWSLATNTGVNLLEPGKTPAENAQFLLFLTAVIKAVYDYQ 360
             CLLHEKPFAG+NGSGKHNNWSL+T+ GVNLLEPGKTP ENAQFL F+ AVIKAV +Y 
Sbjct: 302 LACLLHEKPFAGVNGSGKHNNWSLSTDEGVNLLEPGKTPHENAQFLTFICAVIKAVDEYA 361

Query: 361 DVLRACVATAGNDHRLGANEAPPAIISIFLGDELTGVLDAIVNGYKYEGEH-VEMEIGVD 419
           D+LRA  A +GNDHRLGANEAPPAIISIFLGDEL+ +++ + NG     +   E+ IGV 
Sbjct: 362 DLLRASAANSGNDHRLGANEAPPAIISIFLGDELSDIIEQLKNGKPNSSKQGGELTIGVS 421

Query: 420 VLPHFAKDTTDRNRTSPFAFTGNKFEFRSPGSKLSCAGPNTVLNTIVAKVLDDFADVLEK 479
            LP   KD+TDRNRTSPFAFTGNKFEFR   S LS AGPN V+NTIVA+VL   AD LEK
Sbjct: 422 TLPSLPKDSTDRNRTSPFAFTGNKFEFRMVPSSLSIAGPNVVINTIVAEVLSQMADRLEK 481

Query: 480 ADNFQDALDDLIKNTIKESKAIIFNGDGYSEDWVNEAEKRGLLNLKSTPEAVPTYLAPKN 539
           A++F   L  +++        ++F+G+GYSE+WV EA +RGL NL ST EA+   ++ K 
Sbjct: 482 AEDFHGELQAILQEIAIHHSRVVFDGNGYSEEWVKEAARRGLPNLSSTVEAISALISEKT 541

Query: 540 VELFSKYNVYSETELRSRVDILLDEYCKTINIEALTMIDMAKKDILPAAATYIKELAQTS 599
           +ELF  + V+S TEL SR +I L++Y KTINIEALTM+D+AK+ ILPA   Y  ELA + 
Sbjct: 542 IELFKHHGVFSATELHSRYEIYLEQYSKTINIEALTMVDVAKRQILPAVMRYSTELAHSI 601

Query: 600 KLAK--DCGADTSFEDDLVKRLSSLAAQTYNKLSALEEAEVKARDIN-DVETLANYYHDT 656
              +  D  A+   +  L+  +S L  +   K  AL++A   A+ ++ D      YY D 
Sbjct: 602 NTIRTADPEAEVLAQRSLLNEISPLLKELSFKTKALQDATCAAKQLHGDAYKQGIYYRDV 661

Query: 657 VFVAMGELRAAADEIETLVGEKYWPYPTYGQLLF 690
           VF AM ELR  AD++E LV    WP P+Y ++LF
Sbjct: 662 VFKAMNELRQTADQLEVLVDYDMWPLPSYTKMLF 695


Lambda     K      H
   0.317    0.133    0.391 

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: 1256
Number of extensions: 57
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: 693
Length of database: 697
Length adjustment: 39
Effective length of query: 654
Effective length of database: 658
Effective search space:   430332
Effective search space used:   430332
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 10 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:

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