Alignments for a candidate for pgmA in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Streptacidiphilus oryzae TH49

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_037577608.1 BS73_RS30025 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_000744815.1:WP_037577608.1
          Length = 541

 Score =  766 bits (1977), Expect = 0.0
 Identities = 386/549 (70%), Positives = 444/549 (80%), Gaps = 11/549 (2%)

Query: 2   VANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHI 61
           + + RAG+ A P DLVD+  LVTAYY++ PDPD+ +Q+VAFGTSGHRGS+L   FNE HI
Sbjct: 1   MVDARAGERAIPADLVDVSRLVTAYYALRPDPDEPSQRVAFGTSGHRGSSLHTAFNEWHI 60

Query: 62  LAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTP 121
            A TQAI +YRAAQG  GPLF+G DTH LSEPA  +ALEVLAAN V  ++D  D YTPTP
Sbjct: 61  AATTQAICDYRAAQGIGGPLFLGIDTHALSEPARATALEVLAANGVTVLLDEGDGYTPTP 120

Query: 122 AISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEI 181
           A+SHAILT+ + R    ADGIVVTPSHNPP+DGG KYNPPNGGPA +  T  I  RAN++
Sbjct: 121 AVSHAILTHRQHR----ADGIVVTPSHNPPTDGGFKYNPPNGGPAGSDITGWIQDRANQL 176

Query: 182 LL-ARSMVKRLPLARAL--RTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGAS 238
           +      V+R+P ARAL   T QR+D+ G YVDDLP+ +D+ A+REAG+RIGADPLGGAS
Sbjct: 177 IKDGLDGVRRIPYARALAAETTQRYDFTGRYVDDLPSALDLDAVREAGLRIGADPLGGAS 236

Query: 239 VDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRER 298
           V YWG IA  H LDLTVVNP +D TWRFMTLD DGKIRMDCSSP AMA LI      R++
Sbjct: 237 VGYWGRIAETHRLDLTVVNPEIDPTWRFMTLDWDGKIRMDCSSPYAMASLIE----RRDQ 292

Query: 299 YQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSII 358
           Y IATGNDAD+DRHGIVTPD GLLNPNH+LAVAIEYLY HR  WPA   VGKT+VSSS+I
Sbjct: 293 YAIATGNDADSDRHGIVTPDGGLLNPNHFLAVAIEYLYAHRDGWPAATGVGKTLVSSSMI 352

Query: 359 DRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMA 418
           DRV A +GR+LVEVPVGFKWFVDGL+GA +GFGGEESAGASFLRR G VWTTDKDGI++A
Sbjct: 353 DRVAADLGRKLVEVPVGFKWFVDGLLGAAIGFGGEESAGASFLRRSGHVWTTDKDGILLA 412

Query: 419 LLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAG 478
           LLA+EI AVTG TPSQRY  L   +G P YARIDAPADREQKARL+RLSADQV A  LAG
Sbjct: 413 LLASEITAVTGETPSQRYAKLTERHGAPAYARIDAPADREQKARLSRLSADQVGAESLAG 472

Query: 479 EPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTA 538
           EPITA LT APGNGAA+GG+KV+T +AWFAARPSGTEDVYKIYAESFRGP+HL +VQ  A
Sbjct: 473 EPITAVLTEAPGNGAAVGGVKVSTESAWFAARPSGTEDVYKIYAESFRGPEHLAQVQDAA 532

Query: 539 REVVDRVIG 547
           +E+V+ V+G
Sbjct: 533 KELVNGVLG 541


Lambda     K      H
   0.318    0.135    0.401 

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: 1093
Number of extensions: 44
Number of successful extensions: 4
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: 547
Length of database: 541
Length adjustment: 35
Effective length of query: 512
Effective length of database: 506
Effective search space:   259072
Effective search space used:   259072
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_037577608.1 BS73_RS30025 (alpha-D-glucose phosphate-specific phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01132.hmm
# target sequence database:        /tmp/gapView.1255098.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01132  [M=546]
Accession:   TIGR01132
Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-284  928.1   0.1   8.3e-284  927.9   0.1    1.0  1  NCBI__GCF_000744815.1:WP_037577608.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037577608.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  927.9   0.1  8.3e-284  8.3e-284       3     546 .]       2     541 .]       1     541 [] 0.99

  Alignments for each domain:
  == domain 1  score: 927.9 bits;  conditional E-value: 8.3e-284
                             TIGR01132   3 inpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                           +++raG++a + dl+dv++lv++yy l+pd+++++q+v+fGtsGhrGs+l+++fne hi a +qa+ ++raaq
  NCBI__GCF_000744815.1:WP_037577608.1   2 VDARAGERAIPADLVDVSRLVTAYYALRPDPDEPSQRVAFGTSGHRGSSLHTAFNEWHIAATTQAICDYRAAQ 74 
                                           678********************************************************************** PP

                             TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpsh 148
                                           Gi Gpl++G dthalsepa  ++levlaan+v v+++e ++ytptpavshailt+ +    ++adGiv+tpsh
  NCBI__GCF_000744815.1:WP_037577608.1  75 GIGGPLFLGIDTHALSEPARATALEVLAANGVTVLLDEGDGYTPTPAVSHAILTHRQ----HRADGIVVTPSH 143
                                           *******************************************************99....78********** PP

                             TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvd 221
                                           npp+dGG+kynppnGGpa +++t +i+dran+l+kd+l gv+r+++++al++et+++ d+  +yvddl+  +d
  NCBI__GCF_000744815.1:WP_037577608.1 144 NPPTDGGFKYNPPNGGPAGSDITGWIQDRANQLIKDGLDGVRRIPYARALAAETTQRYDFTGRYVDDLPSALD 216
                                           ************************************************************************* PP

                             TIGR01132 222 laairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllkl 294
                                           l+a+r+aglr+G+dplGGa+v+yw +iae++ ldlt+vn+++d+t+rfmtld+dGkirmdcsspyama+l++ 
  NCBI__GCF_000744815.1:WP_037577608.1 217 LDAVREAGLRIGADPLGGASVGYWGRIAETHRLDLTVVNPEIDPTWRFMTLDWDGKIRMDCSSPYAMASLIER 289
                                           ************************************************************************* PP

                             TIGR01132 295 kdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrk 367
                                           +d+y +a+gndad+drhGivtpd Gllnpnh+lavaieyly hr++w+a + vGktlvss++idrv+adlgrk
  NCBI__GCF_000744815.1:WP_037577608.1 290 RDQYAIATGNDADSDRHGIVTPDGGLLNPNHFLAVAIEYLYAHRDGWPAATGVGKTLVSSSMIDRVAADLGRK 362
                                           ************************************************************************* PP

                             TIGR01132 368 lvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaa 440
                                           lvevpvGfkwfvdGll++++GfGGeesaGasflr+ G vw+tdkdGi+lalla+eitavtG++p+qry +l++
  NCBI__GCF_000744815.1:WP_037577608.1 363 LVEVPVGFKWFVDGLLGAAIGFGGEESAGASFLRRSGHVWTTDKDGILLALLASEITAVTGETPSQRYAKLTE 435
                                           ************************************************************************* PP

                             TIGR01132 441 kyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGt 513
                                           ++G+p+yarida+a+++qkarl++ls+d+v a++laG++ita lt+apGngaa+GG+kv t+ +wfaarpsGt
  NCBI__GCF_000744815.1:WP_037577608.1 436 RHGAPAYARIDAPADREQKARLSRLSADQVGAESLAGEPITAVLTEAPGNGAAVGGVKVSTESAWFAARPSGT 508
                                           ************************************************************************* PP

                             TIGR01132 514 edvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                           edvykiyaesf+g+ehl ++++ a+e+v+ vl+
  NCBI__GCF_000744815.1:WP_037577608.1 509 EDVYKIYAESFRGPEHLAQVQDAAKELVNGVLG 541
                                           *****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (541 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 17.14
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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

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 catabolism of small carbon sources