Alignments for a candidate for glnA in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methylovulum miyakonense HT12

Align glutamine synthetase type III subunit (EC 6.3.1.2) (characterized)
to candidate WP_029151661.1 METMI_RS0112230 glutamine synthetase

Query= metacyc::SYNPCC7942_0169-MONOMER
         (723 letters)



>NCBI__GCF_000384075.1:WP_029151661.1
          Length = 724

 Score = 1104 bits (2856), Expect = 0.0
 Identities = 533/724 (73%), Positives = 621/724 (85%), Gaps = 1/724 (0%)

Query: 1   MSGNAARVNAVHQITNREPLPSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSIKNTIVT 60
           MSGNA R+ A+  ITNR+P+P KPP +L+++WA +VF LSKM+  LPK +FKS+K TI  
Sbjct: 1   MSGNAMRIQAIQTITNRQPMPVKPPSTLDSLWASDVFTLSKMKESLPKEIFKSLKKTIEA 60

Query: 61  GQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKVISEFS 120
             +LD S+AD VA AMKDWA+SKGALYYAHVFYP+TN TAEKHDGFISVQ DG VISEFS
Sbjct: 61  SSELDVSIADVVALAMKDWALSKGALYYAHVFYPLTNATAEKHDGFISVQSDGSVISEFS 120

Query: 121 GKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFVSWTGE 180
           GKVLVQGEPDGSSFPNGGIR TFEARGYT WDVTSPA+IM TDNG+TLCIPTVFVSWTGE
Sbjct: 121 GKVLVQGEPDGSSFPNGGIRSTFEARGYTAWDVTSPAFIMTTDNGATLCIPTVFVSWTGE 180

Query: 181 ALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQRPDLLL 240
           ALDKK PLLR+ AAM+KAA +VL+LLG+T+++ VNSSCGAEQEYFLVDANF + RPDLLL
Sbjct: 181 ALDKKTPLLRANAAMNKAAHRVLSLLGHTDIAPVNSSCGAEQEYFLVDANFVSSRPDLLL 240

Query: 241 AGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAPGQFEI 300
           AGRTLFG   AKGQ+FDDHYFGAIPER+QVFMQDVEE LY+LGIPAKTRHNEVAPGQFEI
Sbjct: 241 AGRTLFGASPAKGQQFDDHYFGAIPERIQVFMQDVEEQLYRLGIPAKTRHNEVAPGQFEI 300

Query: 301 APFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGNATQGN 360
           APFFE+ANVA+DHQQL+MTVL+ TAKKHG +CLLHEKPF GINGSGKHVNWSVGNATQGN
Sbjct: 301 APFFESANVATDHQQLLMTVLRNTAKKHGLVCLLHEKPFKGINGSGKHVNWSVGNATQGN 360

Query: 361 LLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIMSVYLG 420
           LLDPG +PH N+QFL+FCGAVIRGVHK+GPL+RAAIATASNDHRLGANEAPPAIMSVYLG
Sbjct: 361 LLDPGSTPHSNSQFLLFCGAVIRGVHKFGPLLRAAIATASNDHRLGANEAPPAIMSVYLG 420

Query: 421 TQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFEFRAVG 480
           TQL+ VFEQI  G +T S   G+MDLG+  LP   KDAGDRNRTSPFAFTGNRFEFRAVG
Sbjct: 421 TQLDNVFEQISKGEITGSLNAGVMDLGIKTLPTFNKDAGDRNRTSPFAFTGNRFEFRAVG 480

Query: 481 ASQSVSGPLIVLNTILADSLDWIGNRLESELAKGLDLNTAILTVLKEVMEEHGNVIFGGN 540
           + QSV+GPL+ +NT+LADSL+W+ + +ESELAKG  L+  ILTVLKE+++ HG V+FGGN
Sbjct: 481 SGQSVAGPLVAMNTMLADSLNWVADAMESELAKGGTLDATILTVLKEIIDNHGAVVFGGN 540

Query: 541 GYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRFEVYAEQY 600
           GYS EWH+ AVE+RGL NL T ADALPVLKE+ IE LF   GVL+PVEL SRF++YAEQY
Sbjct: 541 GYSAEWHKMAVEERGLRNLRTAADALPVLKEKEIEALFDGLGVLSPVELASRFDIYAEQY 600

Query: 601 ILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIAELTSSLV 660
           IL+IEVEAKL +S+AKT IYPA V+YL+ LSGTI+ L   G++   E+  K++   ++++
Sbjct: 601 ILAIEVEAKLVISMAKTGIYPAVVKYLSDLSGTISCLKSNGVELGNENLIKVSTTLNTMM 660

Query: 661 GAATQLSEAL-EHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPLPTYQEM 719
               +LS AL +H+ +DT  H+Q+CAKT+RPLMD VR+YADALE+EVAD  WP PTYQEM
Sbjct: 661 ATVGKLSNALGQHDFADTEGHMQFCAKTIRPLMDEVRSYADALESEVADELWPFPTYQEM 720

Query: 720 LFIK 723
           LFIK
Sbjct: 721 LFIK 724


Lambda     K      H
   0.316    0.133    0.383 

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: 1446
Number of extensions: 53
Number of successful extensions: 2
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: 723
Length of database: 724
Length adjustment: 40
Effective length of query: 683
Effective length of database: 684
Effective search space:   467172
Effective search space used:   467172
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: 55 (25.8 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