GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Caulobacter crescentus NA1000

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate CCNA_00083 CCNA_00083 phosphoglucomutase/phosphomannomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__Caulo:CCNA_00083
          Length = 546

 Score =  739 bits (1909), Expect = 0.0
 Identities = 381/541 (70%), Positives = 432/541 (79%), Gaps = 9/541 (1%)

Query: 6   RAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAIT 65
           RAG  A PEDLVDL  L+ AY+ I+PD  + AQ+V FGTSGHRGS+L G FNE HILA+T
Sbjct: 5   RAGLRALPEDLVDLDALIGAYFEIKPDVSNPAQKVVFGTSGHRGSSLDGAFNEAHILAVT 64

Query: 66  QAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTPAISH 125
           QAIVEYRAAQG TGPLF+GRDTHGLSEPAW S LEVLAAN V A+VDSRD +TPTPA+SH
Sbjct: 65  QAIVEYRAAQGVTGPLFVGRDTHGLSEPAWRSVLEVLAANGVEALVDSRDGFTPTPAVSH 124

Query: 126 AILTYNR--GRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEILL 183
           AILT+NR  GR    ADG+++TPSHNPP DGGIKYNPP+GGPA + AT+AIA RANE LL
Sbjct: 125 AILTHNRQGGRQ---ADGLLLTPSHNPPRDGGIKYNPPSGGPAGSDATSAIAARANE-LL 180

Query: 184 ARSM--VKRLPLARALRTAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGASVDY 241
           A+ +  VKR+P   A +    +D+LG YVDDLP V+DIAAIR A VRIGADPLGGA+V Y
Sbjct: 181 AQGLAGVKRVPFETARKAVGDYDFLGRYVDDLPAVIDIAAIRAAKVRIGADPLGGAAVAY 240

Query: 242 WGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRERYQI 301
           WG IA RH LDLTVVN  VD  W FM LDTDGKIRMDCSS  AMA LI  M G    Y +
Sbjct: 241 WGAIAERHALDLTVVNDAVDPRWAFMPLDTDGKIRMDCSSSSAMANLIGIMKGGAA-YDV 299

Query: 302 ATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSIIDRV 361
           ATGNDADADRHGIVTPD GL+NPNHYLA AI YL++HRP W A  AVGKT+VSSS+IDRV
Sbjct: 300 ATGNDADADRHGIVTPDGGLMNPNHYLAAAISYLFSHRPGWGADTAVGKTLVSSSMIDRV 359

Query: 362 VAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMALLA 421
           V+G+GR+L+EVPVGFK+FV GL+  ++GFGGEESAGA+FLR DG VWTTDKDGI +ALLA
Sbjct: 360 VSGLGRRLLEVPVGFKYFVPGLLDGSVGFGGEESAGAAFLRHDGGVWTTDKDGIQLALLA 419

Query: 422 AEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAGEPI 481
           AEI AVTG + SQ Y  L  +YG P YAR+DAPA RE+KARL++LS   VSA  LAGE I
Sbjct: 420 AEIQAVTGKSASQLYAGLTDQYGAPAYARVDAPASREEKARLSKLSPSDVSAKTLAGEAI 479

Query: 482 TAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTAREV 541
           T  LT APGNG A+GGLKV T NAWFAARPSGTEDVYK+YAESF G  HL +VQ  AREV
Sbjct: 480 TDILTAAPGNGEAIGGLKVCTQNAWFAARPSGTEDVYKVYAESFLGADHLKQVQAEAREV 539

Query: 542 V 542
           V
Sbjct: 540 V 540


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: 1066
Number of extensions: 36
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: 546
Length adjustment: 36
Effective length of query: 511
Effective length of database: 510
Effective search space:   260610
Effective search space used:   260610
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 CCNA_00083 CCNA_00083 (phosphoglucomutase/phosphomannomutase)
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.32694.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-273  894.6   0.9   1.1e-273  894.5   0.9    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00083  CCNA_00083 phosphoglucomutase/ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00083  CCNA_00083 phosphoglucomutase/phosphomannomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  894.5   0.9  1.1e-273  1.1e-273       3     546 .]       2     545 ..       1     545 [. 0.99

  Alignments for each domain:
  == domain 1  score: 894.5 bits;  conditional E-value: 1.1e-273
                             TIGR01132   3 inpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                           +++raG +a +edl+d+ +l+ +y+ +kpd  n+aqkv fGtsGhrGs+l g+fneahila++qa+ve+raaq
  lcl|FitnessBrowser__Caulo:CCNA_00083   2 MHDRAGLRALPEDLVDLDALIGAYFEIKPDVSNPAQKVVFGTSGHRGSSLDGAFNEAHILAVTQAIVEYRAAQ 74 
                                           89*********************************************************************** PP

                             TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpsh 148
                                           G+tGpl++G+dth+lsepa+ svlevlaan+ve++v++++++tptpavshailt+n+ + + +adG+++tpsh
  lcl|FitnessBrowser__Caulo:CCNA_00083  75 GVTGPLFVGRDTHGLSEPAWRSVLEVLAANGVEALVDSRDGFTPTPAVSHAILTHNR-QGGRQADGLLLTPSH 146
                                           *********************************************************.99************* PP

                             TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvd 221
                                           npp+dGGikynpp+GGpa +++t ai+ ranell+++l+gvkr+++e+a k   v + d++ +yvddl+ v+d
  lcl|FitnessBrowser__Caulo:CCNA_00083 147 NPPRDGGIKYNPPSGGPAGSDATSAIAARANELLAQGLAGVKRVPFETARK--AVGDYDFLGRYVDDLPAVID 217
                                           *************************************************99..899***************** PP

                             TIGR01132 222 laairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllkl 294
                                           +aair a++r+G+dplGGa+v yw  iae++ ldlt+vn+avd+ + fm ld+dGkirmdcss  ama+l+ +
  lcl|FitnessBrowser__Caulo:CCNA_00083 218 IAAIRAAKVRIGADPLGGAAVAYWGAIAERHALDLTVVNDAVDPRWAFMPLDTDGKIRMDCSSSSAMANLIGI 290
                                           ********************************************************************99985 PP

                             TIGR01132 295 k...dkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadl 364
                                                 yd+a+gndadadrhGivtpd Gl+npnhyla ai+yl++hr++w+a++avGktlvss++idrvv+ l
  lcl|FitnessBrowser__Caulo:CCNA_00083 291 MkggAAYDVATGNDADADRHGIVTPDGGLMNPNHYLAAAISYLFSHRPGWGADTAVGKTLVSSSMIDRVVSGL 363
                                           412268******************************************************************* PP

                             TIGR01132 365 grklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqryde 437
                                           gr+l+evpvGfk+fv Glldgs+GfGGeesaGa+flr+dG vw+tdkdGi lallaaei avtGk+ +q y  
  lcl|FitnessBrowser__Caulo:CCNA_00083 364 GRRLLEVPVGFKYFVPGLLDGSVGFGGEESAGAAFLRHDGGVWTTDKDGIQLALLAAEIQAVTGKSASQLYAG 436
                                           ************************************************************************* PP

                             TIGR01132 438 laakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarp 510
                                           l+ +yG+p+yar+da+a++++karl+klsp +vsa+tlaG+ait  lt+apGng aiGGlkv t+++wfaarp
  lcl|FitnessBrowser__Caulo:CCNA_00083 437 LTDQYGAPAYARVDAPASREEKARLSKLSPSDVSAKTLAGEAITDILTAAPGNGEAIGGLKVCTQNAWFAARP 509
                                           ************************************************************************* PP

                             TIGR01132 511 sGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                           sGtedvyk+yaesf g++hlk+++ ea+e+v  +lk
  lcl|FitnessBrowser__Caulo:CCNA_00083 510 SGTEDVYKVYAESFLGADHLKQVQAEAREVVAGALK 545
                                           *******************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (546 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.41
//
[ok]

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