GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Marinobacter adhaerens HP15

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing

Query= BRENDA::P22106
         (554 letters)



>lcl|FitnessBrowser__Marino:GFF1957 HP15_1914 asparagine synthase,
           glutamine-hydrolyzing
          Length = 632

 Score =  147 bits (371), Expect = 1e-39
 Identities = 122/394 (30%), Positives = 188/394 (47%), Gaps = 56/394 (14%)

Query: 1   MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVN- 57
           MC I G     T  D  +    A  + + + HRGPD +G++   +  L H+RLSI+D++ 
Sbjct: 1   MCGIAGFLRTGTLPDREQHHLWAERMGQAIAHRGPDANGVHIDQDVALVHQRLSILDLSS 60

Query: 58  AGAQPLYNQQKTHVLAVNGEIYNHQALRAEYG-DRYQFQTGSDCEVILALYQEKGPEFLD 116
           AG QP+ +    +++  NGEIYN ++LR     D + F+T +D EV+LALY   G   L 
Sbjct: 61  AGNQPMASSCGRYIIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLR 120

Query: 117 DLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL--VPVCR---- 170
            L GMFAFA++D++  +  IGRD LG  PLY   D  GQ +  SE+KAL   PV R    
Sbjct: 121 QLNGMFAFAIWDAKTKSLFIGRDRLGKKPLYY-TDTDGQFFFGSEIKALFATPVVRPALR 179

Query: 171 --TIKEF-------------------PAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTD- 208
              IK+F                   P G  +   +G I    + D          V+D 
Sbjct: 180 PDAIKDFFVYQYIPDPKTIYANVHKLPPGHCMEVCEGRISVRKYWDLSFRPVEGRTVSDI 239

Query: 209 KNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQL 268
           K  L   ++++V+  ++SDVP G  LSGG+DSS +  +    +++ V             
Sbjct: 240 KAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVT------------ 287

Query: 269 HSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETY--DVTTI 324
            +  +G       ++K A  VA    T HH   FTV+E    + D +  I  +  +    
Sbjct: 288 -TCTIGFDDEKFDEIKYADLVARQFKTDHHV--FTVKE---TVADNLVGISRFFDEPFAD 341

Query: 325 RASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGY 358
            +  P + +S+  +   + + L+G+G DE F GY
Sbjct: 342 PSFVPTFFVSQLARTQ-VTVALAGDGGDENFAGY 374



 Score = 41.2 bits (95), Expect = 1e-07
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 388 RANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAW 447
           + ++   A  +E R P LD + ++ A  I    K+ GN K  KH+L+ECF   L   + +
Sbjct: 497 KVDRMSMANSLETRAPLLDYRVVEYAAGIPSALKLKGNCK--KHVLKECFSDLLDEDILY 554

Query: 448 RQKEQFS 454
           R+K  FS
Sbjct: 555 RKKMGFS 561


Lambda     K      H
   0.319    0.135    0.407 

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: 797
Number of extensions: 41
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 554
Length of database: 632
Length adjustment: 37
Effective length of query: 517
Effective length of database: 595
Effective search space:   307615
Effective search space used:   307615
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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