GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Magnetospirillum magneticum AMB-1

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_000009985.1:WP_011382978.1
          Length = 553

 Score =  125 bits (315), Expect = 2e-33
 Identities = 88/242 (36%), Positives = 127/242 (52%), Gaps = 6/242 (2%)

Query: 1   MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60
           +LEL+  AK  GA   +   DL +E G    +LG + +GKT+L+ LMAGL +P  G +  
Sbjct: 3   ILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLL 62

Query: 61  DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVR--KAAEL 118
            G  V G P   R V  V+Q +   P LTV  NIA  +     DA+  +R+ R  K   +
Sbjct: 63  RGKPVDG-PGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIGM 119

Query: 119 LKLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIF 178
           + L+   +R P  LSGG +QR A+ARAL  +  ++L+DEPL+ LD   R +L++E+  I+
Sbjct: 120 VGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIW 179

Query: 179 AQSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLN 238
            Q     +  T +  EALLL      LN G    FGP+ +V   P     A + +DP   
Sbjct: 180 EQEKKTVILITNDVDEALLLADRIIPLNPGPGATFGPSFKV-NLPRPRDRAAVNSDPDFK 238

Query: 239 TL 240
            L
Sbjct: 239 RL 240



 Score = 78.2 bits (191), Expect = 5e-19
 Identities = 59/216 (27%), Positives = 102/216 (47%), Gaps = 16/216 (7%)

Query: 17  IYPT-----------DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDV 65
           IYPT           DL + +G    L+G +  GK++++ + AGL   + G +  DG +V
Sbjct: 301 IYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREV 360

Query: 66  TGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDRE--VRKAAELLKLTP 123
           +     +   A+V+Q    +P LT   N+A  +      A+  +R   V    E + L  
Sbjct: 361 SEAGPDR---AVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYYLERVGLGD 417

Query: 124 YLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGA 183
            +D+   ++S G +QR  +ARA   +  L+L+DEP   LD   R EL+E L +++ ++  
Sbjct: 418 SMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRV 477

Query: 184 IFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEV 219
             +  T +  EA+LL      +  G   + G  + V
Sbjct: 478 TAICVTHDVDEAILLADKVVMMTNGPNARIGKVLNV 513


Lambda     K      H
   0.319    0.136    0.392 

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: 467
Number of extensions: 24
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: 358
Length of database: 553
Length adjustment: 32
Effective length of query: 326
Effective length of database: 521
Effective search space:   169846
Effective search space used:   169846
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: 51 (24.3 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:

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