GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 201480 SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__MR1:201480
          Length = 550

 Score =  645 bits (1665), Expect = 0.0
 Identities = 321/548 (58%), Positives = 405/548 (73%), Gaps = 5/548 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           MAIH RAGQ A Q DL+N+ +L + YY +KP    AE  V FGTSGHRG+A + SFN+ H
Sbjct: 1   MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           I AI QA+ + R    I GP ++G DTHALS  A++S +EVLAAN V V +Q+N+GFTPT
Sbjct: 61  IWAITQAVVDYRQSVNIEGPLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPT 120

Query: 121 PAVSNAILVHN----KKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176
           P VS+AI+  N    + G  L+DG++ITPSHNPP+DGGIKYNPP+GGPA+ N+T  +E R
Sbjct: 121 PVVSHAIICANHAAAQNGALLSDGLIITPSHNPPQDGGIKYNPPHGGPAEGNITAWIESR 180

Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
           AN  L   L+GV +++   A+ASG+V A+DL+ P+V  L ++VDM AI KA L LGVDPL
Sbjct: 181 ANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGVDPL 240

Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296
           GGSGI YW  IA+HY +++TLVND+VD +F FM LDKDG IRMDCSS  AMAGLLA ++ 
Sbjct: 241 GGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKES 300

Query: 297 FDLAFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355
           FDL   NDPDYDRHGIV P  GLM+PNHYLAVAI+YL  HRP W   +A+GKTLVSSA+I
Sbjct: 301 FDLCVGNDPDYDRHGIVCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALI 360

Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415
           D++    G+KL+EVPVGFKWFVDGL + +  FGGEESAGA+FLR DGT W TDKDG I+ 
Sbjct: 361 DKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGEESAGAAFLRRDGTTWCTDKDGFILV 420

Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475
           LLAAE+ AVTGK P + + EL A+FG   Y R+ +  +   KA  +KL+ + ++A+ LAG
Sbjct: 421 LLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLNATMLAG 480

Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535
           + I A LT APGN ASIGG+KV T NGWFAARPSGTE  +KIY ESF+ E+H  +I K+A
Sbjct: 481 EKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDA 540

Query: 536 VEIVSEVL 543
             ++ + L
Sbjct: 541 QALIDKAL 548


Lambda     K      H
   0.316    0.134    0.395 

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: 885
Number of extensions: 35
Number of successful extensions: 3
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: 546
Length of database: 550
Length adjustment: 36
Effective length of query: 510
Effective length of database: 514
Effective search space:   262140
Effective search space used:   262140
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate 201480 SO2336 (phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file))
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.23772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.2e-261  853.0   0.9   4.8e-261  852.8   0.9    1.0  1  lcl|FitnessBrowser__MR1:201480  SO2336 phosphoglucomutase, alpha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201480  SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  852.8   0.9  4.8e-261  4.8e-261       1     545 [.       1     548 [.       1     549 [. 0.99

  Alignments for each domain:
  == domain 1  score: 852.8 bits;  conditional E-value: 4.8e-261
                       TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 
                                     mai++raGq a q dl++++kl+++yy++kp+ + a+q+v+fGtsGhrG+a +g+fn+ hi ai+qavv++r+   i G
  lcl|FitnessBrowser__MR1:201480   1 MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDHIWAITQAVVDYRQSVNIEG 79 
                                     89***************************************************************************** PP

                       TIGR01132  80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkea...ladGivitpshnppedGG 155
                                     pl++G dthals  a+vs++evlaan+v v +q+n+++tptp vshai+  n++  ++   l+dG++itpshnpp+dGG
  lcl|FitnessBrowser__MR1:201480  80 PLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPTPVVSHAIICANHAAAQNgalLSDGLIITPSHNPPQDGG 158
                                     **************************************************9986544322378**************** PP

                       TIGR01132 156 ikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGv 234
                                     ikynpp+GGpae+++t +ie ran++l++ lkgv +l ++ al+s+ v++ dl++pyv+dl +vvd+ ai ka+l+lGv
  lcl|FitnessBrowser__MR1:201480 159 IKYNPPHGGPAEGNITAWIESRANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGV 237
                                     ******************************************************************************* PP

                       TIGR01132 235 dplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGi 313
                                     dplGG+g++yw +ia++y++d+tlvn++vd++f fm+ldkdGkirmdcsspyamagll+ k+ +dl +gnd+d+drhGi
  lcl|FitnessBrowser__MR1:201480 238 DPLGGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKESFDLCVGNDPDYDRHGI 316
                                     ******************************************************************************* PP

                       TIGR01132 314 vtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGe 392
                                     v p +Gl++pnhylavai+yl +hr++w++++a+Gktlvssalid++    g+kl+evpvGfkwfvdGl ++++ fGGe
  lcl|FitnessBrowser__MR1:201480 317 VCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALIDKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGE 395
                                     ******************************************************************************* PP

                       TIGR01132 393 esaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevs 471
                                     esaGa+flr+dGt+w+tdkdG il llaae++avtGk+p+qr++el a++G+ +y+rid++ + ++ka+++kl +d++ 
  lcl|FitnessBrowser__MR1:201480 396 ESAGAAFLRRDGTTWCTDKDGFILVLLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLN 474
                                     ******************************************************************************* PP

                       TIGR01132 472 attlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                     at laG+ i a lt+apGn+a+iGG+kvtt +gwfaarpsGte ++kiy esf  e+hl ei k+a++++d++l
  lcl|FitnessBrowser__MR1:201480 475 ATMLAGEKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDAQALIDKAL 548
                                     **********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (550 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.54
//
[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