GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Thiohalospira halophila HL 3

Align Phosphoglucomutase-1; PGM 1; Glucose phosphomutase 1; EC 5.4.2.2 (characterized)
to candidate WP_093428782.1 BM272_RS10670 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= SwissProt::P38652
         (562 letters)



>NCBI__GCF_900112605.1:WP_093428782.1
          Length = 543

 Score =  580 bits (1496), Expect = e-170
 Identities = 301/560 (53%), Positives = 398/560 (71%), Gaps = 20/560 (3%)

Query: 4   IVTVKTQAYPDQKPGTSGLRKRVKVFQGNANYAENFIQSIVSTVEPALRQEATLVVGGDG 63
           I TV TQ + DQKPGTSGLRKRV  FQ   NY ENF+QSI+   E    +  TLV+GGDG
Sbjct: 3   IQTVATQPFDDQKPGTSGLRKRVTRFQ-QPNYLENFVQSILDVGEGL--RGGTLVLGGDG 59

Query: 64  RFYMTEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGP 123
           R+Y   AIQ I+R+AAA+G+GR+++G++G+LSTPAVS IIRK +A GGI+L+ASHNPGGP
Sbjct: 60  RYYNETAIQTILRMAAAHGVGRVLVGRDGLLSTPAVSAIIRKRRADGGIVLSASHNPGGP 119

Query: 124 NGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKP 183
            GDFGIKFN +NGGPAPE++T+ I+Q S+T++EY I     +DL   G  +       + 
Sbjct: 120 EGDFGIKFNTANGGPAPESVTEAIYQRSRTLDEYRITDTGDIDLSREGAVEI------QG 173

Query: 184 FTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGA 243
            TVE++D V  YA ++  +FD  A+  +++   RL  R DAMH + GPY ++IL E LGA
Sbjct: 174 TTVEVIDPVADYAALMEELFDMEAIAAMIADGFRL--RFDAMHAITGPYARRILEERLGA 231

Query: 244 PANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEH-DFGAAFDGDGDRNMILGKHGF 302
           PA S +N  PL DFGG HPDPNL +A +LV  M   +  D GAA DGDGDRNMILG   F
Sbjct: 232 PAGSVINAEPLPDFGGGHPDPNLVHAPELVALMYGPDAPDLGAASDGDGDRNMILGPD-F 290

Query: 303 FVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIASYETPTGWKFF 362
           FV PSDS+A +AAN    P +   G+RG ARSMPTS A DRVA A  +  YETPTGWKFF
Sbjct: 291 FVTPSDSLAFLAANATCAPGYAG-GIRGIARSMPTSAAADRVAEALGVPCYETPTGWKFF 349

Query: 363 GNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQRVEDILKDHWQKFGR 422
           GNL+DA +++LCGEESFGTGS H+REKDGLWAVL WL+ILA R++ V D+L+DHWQ+FGR
Sbjct: 350 GNLLDADRVTLCGEESFGTGSAHVREKDGLWAVLFWLNILAVRQRGVGDLLRDHWQRFGR 409

Query: 423 NFFTRYDYEEVEAEGANKMMKDLEALMLDRSFVGKQFSANDKVYTVEKADNFEYSDPVDG 482
           N ++RYDYE V+AE A +M++ L   + D    G+ F+      TV  AD+F Y+DP+DG
Sbjct: 410 NVYSRYDYEGVDAEAAGRMVEGLRGRLAD--LPGQSFNG----LTVTAADDFAYTDPIDG 463

Query: 483 SISKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDAAKINQDPQVMLAPLISI 542
           S +++QGLR+ F  G R++FRLSGTG+ GAT+R+Y++++E +  + ++    +LAPL + 
Sbjct: 464 SRAEHQGLRIFFQGGERLVFRLSGTGTEGATLRVYLEAFEGNPERQDRPTAELLAPLTAA 523

Query: 543 ALKVSQLQERTGRTAPTVIT 562
           A  ++ ++  TGR  P VIT
Sbjct: 524 AEALAGIRSHTGRAEPDVIT 543


Lambda     K      H
   0.319    0.137    0.397 

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: 866
Number of extensions: 52
Number of successful extensions: 10
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: 562
Length of database: 543
Length adjustment: 36
Effective length of query: 526
Effective length of database: 507
Effective search space:   266682
Effective search space used:   266682
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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