GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Magnetospirillum magneticum AMB-1

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_011382566.1 AMB_RS00600 asparagine synthase (glutamine-hydrolyzing)

Query= BRENDA::P22106
         (554 letters)



>lcl|NCBI__GCF_000009985.1:WP_011382566.1 AMB_RS00600 asparagine
           synthase (glutamine-hydrolyzing)
          Length = 639

 Score =  152 bits (384), Expect = 4e-41
 Identities = 131/395 (33%), Positives = 189/395 (47%), Gaps = 59/395 (14%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MC IFG+       VE    A  +   + HRGPD +GI+A     L + RL++VD   G+
Sbjct: 1   MCGIFGMVRGGGRPVESNVLAA-MKTALHHRGPDGNGIFAEGPVGLGNTRLAVVDTAGGS 59

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGD-RYQFQTGSDCEVILALYQEKGPEFLDDLQ 119
           QP+ +      +  NGE++NH  LRAE     + F+T SD EV+LA +   G + +    
Sbjct: 60  QPVIDPSSGAAIVYNGELFNHLELRAELESVGWCFRTHSDTEVVLAAFCVWGEDCVLRFN 119

Query: 120 GMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRT-------- 171
           GM+AFA++D +     I RD  GI PLY+     G L  ASE KAL+P+           
Sbjct: 120 GMYAFAVFDPKARRVFIARDPAGIKPLYLTETADG-LAFASEAKALLPIAGRRPDWQALW 178

Query: 172 -----------------IKEFPAGSYLWSQDGEIRSY------YHRDWFDYDAVKDNVTD 208
                            I +FPAGS  W  D E+ +       Y +  F   A       
Sbjct: 179 GYLTYGYMAPDCSPFAGITKFPAGSLAWI-DLELPAARLAVRPYWQPRFGCGAPLAEGEA 237

Query: 209 KNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQL 268
            + L   L  +VK  LMSDVP G+ LSGGLDSS ++     YAARR       +A    +
Sbjct: 238 VDRLDALLSQAVKHELMSDVPVGLFLSGGLDSSAVA----YYAARR-----HGQA----I 284

Query: 269 HSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFT---VQEGLDAIRDVIYHIETYDVTT 323
            SF +    +   +   A+ VA HLG  H E+ F+   V+EGL  + + +   E +  +T
Sbjct: 285 SSFGLAFEETTHDESNDARTVARHLGIEHKELMFSPALVREGLRRVTETM--DEPFGDST 342

Query: 324 IRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGY 358
           +    P+ ++SR  +   + +VL+G G DEV  GY
Sbjct: 343 V---VPLLMLSRFARE-HVTVVLTGWGGDEVLAGY 373



 Score = 39.7 bits (91), Expect = 4e-07
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 3/82 (3%)

Query: 381 LHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAY 440
           LH     +A++   A  +EARVP L+K+ LD A+ +    KM G     K +L++    +
Sbjct: 490 LHGNGLFQADRMTMAASLEARVPLLNKQMLDFALPLPAGLKMAGG--TPKGLLKKALAPH 547

Query: 441 LPASVAWRQKEQFSDGVGYSWI 462
           LP ++  + K+ F    G+ W+
Sbjct: 548 LPPAILSKPKKGFGPPSGH-WV 568


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: 812
Number of extensions: 43
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 554
Length of database: 639
Length adjustment: 37
Effective length of query: 517
Effective length of database: 602
Effective search space:   311234
Effective search space used:   311234
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 preprint 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