Alignments for a candidate for pgmA in Frankia alni ACN14A

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Frankia alni ACN14A

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_011603108.1 FRAAL_RS08395 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_000058485.1:WP_011603108.1
          Length = 555

 Score =  671 bits (1730), Expect = 0.0
 Identities = 352/556 (63%), Positives = 403/556 (72%), Gaps = 14/556 (2%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +PRAGQPA PEDL+D+  L+ AY  + PDP D AQ+V+FGTSGHRGSAL G+FN  H
Sbjct: 1   MPISPRAGQPAAPEDLIDVDALLAAYQDVHPDPADPAQRVSFGTSGHRGSALRGSFNADH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           ILA TQAI ++RAA G  GPLF+G DTH LS PA  SALEVL AN V   +      TPT
Sbjct: 61  ILATTQAICDFRAAAGVDGPLFLGIDTHALSAPALASALEVLVANGVAVRIAPDGEATPT 120

Query: 121 PAISHAILTYNRGRT---------EALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAAT 171
           P ISHAIL +NR R            LADGIVVTPSHNPP+DGG KYNP +GGPADTA T
Sbjct: 121 PVISHAILGHNRDRGATAAGGASGRGLADGIVVTPSHNPPADGGFKYNPTHGGPADTAVT 180

Query: 172 TAIAKRANEILLAR-SMVKRLPLARALRTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIG 230
             I  RAN +L A  + V R+P A+A   A  HDY+G YV DL +VVD+ AIR AGVRIG
Sbjct: 181 KVIQDRANALLEAGLAGVARVPYAQARAAAAVHDYVGAYVADLGDVVDLDAIRAAGVRIG 240

Query: 231 ADPLGGASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIR 290
            DPLGGAS+ YW  +A R+ LDL VVN  VD T+ FMT D DGKIRMD SSP AMA L+R
Sbjct: 241 VDPLGGASLVYWQALAERYKLDLDVVNTTVDPTFSFMTTDWDGKIRMDPSSPYAMASLLR 300

Query: 291 TMFGNRERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGK 350
               +   + +A  NDADADRHGIVTP  GLLNPNHYL+ AI YL+ HR  WPAG A+GK
Sbjct: 301 ----HAGSFDVAVANDADADRHGIVTPGAGLLNPNHYLSAAIAYLFGHRTGWPAGTAIGK 356

Query: 351 TVVSSSIIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTT 410
           T+VSSS+IDRV AGIGR +VEVPVGFKWFVDGL   TLGFGGEESAGASFLRR G VWTT
Sbjct: 357 TLVSSSMIDRVGAGIGRAVVEVPVGFKWFVDGLTDGTLGFGGEESAGASFLRRGGGVWTT 416

Query: 411 DKDGIIMALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQ 470
           DKDG+I  LLAAE+ AVTG  P   Y  L   +G P Y R+DAPA   QK  LA L+   
Sbjct: 417 DKDGLIACLLAAEMTAVTGRDPGALYQELTELHGAPAYRRVDAPATAAQKKILAALTPAS 476

Query: 471 VSATELAGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQH 530
           ++AT LAG P+TA L  APGNGAA+GG+KV TA+AWFAARPSGTEDVYKIYAESFRGP+H
Sbjct: 477 LAATTLAGSPVTAALAQAPGNGAAIGGVKVVTADAWFAARPSGTEDVYKIYAESFRGPEH 536

Query: 531 LVEVQQTAREVVDRVI 546
           L EV   A+ +VD  +
Sbjct: 537 LEEVITQAQAIVDAAL 552


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: 1078
Number of extensions: 48
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: 555
Length adjustment: 36
Effective length of query: 511
Effective length of database: 519
Effective search space:   265209
Effective search space used:   265209
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: 53 (25.0 bits)

Align candidate WP_011603108.1 FRAAL_RS08395 (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.8056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-262  856.6   4.4   3.9e-262  856.4   4.4    1.0  1  lcl|NCBI__GCF_000058485.1:WP_011603108.1  FRAAL_RS08395 alpha-D-glucose ph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011603108.1  FRAAL_RS08395 alpha-D-glucose phosphate-specific phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  856.4   4.4  3.9e-262  3.9e-262       1     545 [.       1     552 [.       1     553 [. 0.97

  Alignments for each domain:
  == domain 1  score: 856.4 bits;  conditional E-value: 3.9e-262
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               m i praGq+a +edl+dv +l+a+y  ++pd+ ++aq+v+fGtsGhrGsal+g+fn  hila +qa+ 
  lcl|NCBI__GCF_000058485.1:WP_011603108.1   1 MPISPRAGQPAAPEDLIDVDALLAAYQDVHPDPADPAQRVSFGTSGHRGSALRGSFNADHILATTQAIC 69 
                                               5689***************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkke.. 136
                                               + raa G+ Gpl++G dthals pa  s+levl+an+v v +      tptp +shail +n+ + +  
  lcl|NCBI__GCF_000058485.1:WP_011603108.1  70 DFRAAAGVDGPLFLGIDTHALSAPALASALEVLVANGVAVRIAPDGEATPTPVISHAILGHNRDRGAta 138
                                               **************************************************************9886422 PP

                                 TIGR01132 137 .......aladGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekal 198
                                                      +ladGiv+tpshnpp dGG+kynp +GGpa+t+vtk+i+dran+ll+++l+gv r+++++a 
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 139 aggasgrGLADGIVVTPSHNPPADGGFKYNPTHGGPADTAVTKVIQDRANALLEAGLAGVARVPYAQAR 207
                                               2222222689**********************************************************9 PP

                                 TIGR01132 199 ksetvkekdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatf 267
                                               ++  +  +d+v  yv+dl dvvdl+air ag+r+GvdplGGa++ yw+ +ae+y+ldl +vn +vd+tf
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 208 AA--AAVHDYVGAYVADLGDVVDLDAIRAAGVRIGVDPLGGASLVYWQALAERYKLDLDVVNTTVDPTF 274
                                               95..5568************************************************************* PP

                                 TIGR01132 268 rfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylyk 336
                                                fmt d+dGkirmd sspyama+ll+    +d+a++ndadadrhGivtp +Gllnpnhyl+ ai yl+ 
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 275 SFMTTDWDGKIRMDPSSPYAMASLLRHAGSFDVAVANDADADRHGIVTPGAGLLNPNHYLSAAIAYLFG 343
                                               ********************************************************************* PP

                                 TIGR01132 337 hrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGt 405
                                               hr +w+a +a+Gktlvss++idrv+a +gr +vevpvGfkwfvdGl dg+lGfGGeesaGasflr+ G 
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 344 HRTGWPAGTAIGKTLVSSSMIDRVGAGIGRAVVEVPVGFKWFVDGLTDGTLGFGGEESAGASFLRRGGG 412
                                               ********************************************************************* PP

                                 TIGR01132 406 vwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsatt 474
                                               vw+tdkdG+i +llaae+tavtG++p+  y+el++ +G+p+y+r+da+at+aqk+ l+ l+p +++att
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 413 VWTTDKDGLIACLLAAEMTAVTGRDPGALYQELTELHGAPAYRRVDAPATAAQKKILAALTPASLAATT 481
                                               ********************************************************************* PP

                                 TIGR01132 475 laGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivde 543
                                               laG ++ta l++apGngaaiGG+kv+t+++wfaarpsGtedvykiyaesf+g+ehl+e+ ++a++ivd 
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 482 LAGSPVTAALAQAPGNGAAIGGVKVVTADAWFAARPSGTEDVYKIYAESFRGPEHLEEVITQAQAIVDA 550
                                               *******************************************************************98 PP

                                 TIGR01132 544 vl 545
                                               +l
  lcl|NCBI__GCF_000058485.1:WP_011603108.1 551 AL 552
                                               76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (555 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.84
//
[ok]

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:

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 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