Alignments for a candidate for scrP in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for scrP in Shewanella sp. ANA-3

Align sucrose phosphorylase (EC 2.4.1.7) (characterized)
to candidate 7022815 Shewana3_0066 sucrose phosphorylase (RefSeq)

Query= CAZy::CAA80424.1
         (488 letters)



>FitnessBrowser__ANA3:7022815
          Length = 494

 Score =  545 bits (1405), Expect = e-159
 Identities = 279/474 (58%), Positives = 341/474 (71%), Gaps = 2/474 (0%)

Query: 1   MKNSVQLITYVDRLSGGGFPELRALLDGRLQGLFGGVHALPFFNPIDGADAGFDPTDHTI 60
           MKN VQLITYVDR++G G  +L+ALLD  L GLFGGVH LPF+ PIDG+DAGFDP DH  
Sbjct: 1   MKNQVQLITYVDRITGAGLKQLKALLDNELDGLFGGVHLLPFYYPIDGSDAGFDPIDHVQ 60

Query: 61  VDPRLGSWDDVRALAGSVEIMADLIVNHVSAQSSWFQDFIAKGSDSEFADMFMTFGKAFP 120
           VD RLG WDDV+++  + +IMADLIVNH+SA+S  F+D +  G  S + D+F+T  K FP
Sbjct: 61  VDSRLGDWDDVKSIGEAFDIMADLIVNHMSAESPEFKDVLKHGKQSVYWDLFLTKDKVFP 120

Query: 121 RGASEQDLLNIYRPRLGCRFQRPRLQIGSQRMLWTTFTPQQIDIDVHSAHGALYLETILD 180
            G SEQD   IYRPR G  F    L  GS    WTTFT  QIDIDV+SA G  YL  +L 
Sbjct: 121 EGLSEQDQKAIYRPRPGSCFSTYTLADGSTEEFWTTFTRNQIDIDVNSAAGKDYLNRVLA 180

Query: 181 RFAEANVTAIRLDAAGYAIKKAGTSCFMIDETYAFLAKLAEKARDRGMEVLVEIHSYYRD 240
           RF  + V  IRLDAAGYAIKK GTSCFMI+E++ F+ KLA++A + GM  L EIHS++  
Sbjct: 181 RFNHSKVNLIRLDAAGYAIKKPGTSCFMIEESFEFVDKLAKQANELGMTTLAEIHSHHMT 240

Query: 241 QIEIASKVDRVYDFALPPLILHSLFTGDATALARWLEISPHNAITVLDTHDGIGVIDVGA 300
           QI+IA +VD VYDFALPPLILH+LF+ D +AL+ WL+++P N ITVLDTHDGIG+IDVG 
Sbjct: 241 QIDIAKRVDMVYDFALPPLILHTLFSQDCSALSHWLDMAPRNCITVLDTHDGIGIIDVGP 300

Query: 301 HSDGRPGLLEPQAIDHLVEEIHRRSEGQSRLATGAAASNLDLYQVNCTYYDALGRNDDDY 360
             DG  GLL  + ID+LVE IH  S+G+S  ATGAAASN+DLYQ+NCTYYDALG+ND DY
Sbjct: 301 -MDGLRGLLNEKQIDNLVETIHGNSQGESLQATGAAASNVDLYQINCTYYDALGQNDLDY 359

Query: 361 LIARAIQFFAPGIPQVYYVGLLGGINDMELLGKTGVGRDINRHFYEDREIDLALESPLVK 420
           L+ARAIQFFAPGIPQVYY GLL   NDM LL +T VGRDINR +    ++  AL+ P+VK
Sbjct: 360 LMARAIQFFAPGIPQVYYTGLLAIPNDMTLLNQTHVGRDINRPYLNREKVQQALQKPVVK 419

Query: 421 RLSDLIRFRNTHPAFNGSFEVATDDTGSLVLSWNLNTEFAQLVVSFSQGKATIT 474
            L  LI+ RN   AFNG F +A     +L L+W+     A L + F+  +  IT
Sbjct: 420 ALIQLIKLRNNSAAFNGRFSMAASGK-TLTLTWSAQNASASLSLDFAHKQGLIT 472


Lambda     K      H
   0.322    0.139    0.417 

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: 669
Number of extensions: 16
Number of successful extensions: 2
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: 488
Length of database: 494
Length adjustment: 34
Effective length of query: 454
Effective length of database: 460
Effective search space:   208840
Effective search space used:   208840
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 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 7022815 Shewana3_0066 (sucrose phosphorylase (RefSeq))
to HMM TIGR03852 (gtfA: sucrose phosphorylase (EC 2.4.1.7))

# 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/TIGR03852.hmm
# target sequence database:        /tmp/gapView.27358.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03852  [M=470]
Accession:   TIGR03852
Description: sucrose_gtfA: sucrose phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.6e-136  439.0   0.0   1.2e-135  438.7   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7022815  Shewana3_0066 sucrose phosphoryl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7022815  Shewana3_0066 sucrose phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.7   0.0  1.2e-135  1.2e-135       1     464 [.       3     468 ..       3     473 .. 0.95

  Alignments for each domain:
  == domain 1  score: 438.7 bits;  conditional E-value: 1.2e-135
                         TIGR03852   1 nkvmlityadsl.GknlkelekvleeelkdavGGvhllpff.p.ssgdrGfapsdyekvdeafGdwedvealsekyy 74 
                                       n+v lity d + G  lk+l+  l++el++  GGvhllpf+ p   +d Gf p+d+ +vd+++Gdw+dv++++e ++
  lcl|FitnessBrowser__ANA3:7022815   3 NQVQLITYVDRItGAGLKQLKALLDNELDGLFGGVHLLPFYyPiDGSDAGFDPIDHVQVDSRLGDWDDVKSIGEAFD 79 
                                       8999******86599************************974634579***************************** PP

                         TIGR03852  75 lmfdfminhiskeseyykdflekkdeskykdlfirykdfwpegrpteedvdliykrkdrapyqevefadGstekvwn 151
                                       +m d ++nh+s+es+ +kd l++ ++s y dlf+  ++ +peg   e+d  +iy+ ++ + + + ++adGste+ w+
  lcl|FitnessBrowser__ANA3:7022815  80 IMADLIVNHMSAESPEFKDVLKHGKQSVYWDLFLTKDKVFPEGLS-EQDQKAIYRPRPGSCFSTYTLADGSTEEFWT 155
                                       *****************************************9975.66889************************** PP

                         TIGR03852 152 tfgeeqidldvtkevtkkfikenlenlaekGaslirldafayavkkldtndffvepeiwelldevrdilaakdaeil 228
                                       tf  +qid+dv++   k++++  l  + +  ++lirlda  ya+kk +t++f++e e +e++d+  +++++ +++ l
  lcl|FitnessBrowser__ANA3:7022815 156 TFTRNQIDIDVNSAAGKDYLNRVLARFNHSKVNLIRLDAAGYAIKKPGTSCFMIE-ESFEFVDKLAKQANELGMTTL 231
                                       ******************************************************9.679****************** PP

                         TIGR03852 229 peihehytiqlkiaekdyyvydfalplvvlyslysgkterladwlkkspmkqfttldthdGiGvvdv......kdll 299
                                        eih h+  q+ ia++   vydfalp ++l++l+s  +  l++wl ++p+   t ldthdGiG++dv      + ll
  lcl|FitnessBrowser__ANA3:7022815 232 AEIHSHHMTQIDIAKRVDMVYDFALPPLILHTLFSQDCSALSHWLDMAPRNCITVLDTHDGIGIIDVgpmdglRGLL 308
                                       ******************************************************************8665555679* PP

                         TIGR03852 300 tdeeidatkeelykvGanvkkiyssaeynnldiyqinstyysalGdddkayllarvvqvfapGipqvyyvGllaGkn 376
                                       ++++id   e ++          + a+  n+d+yqin+tyy alG++d  yl+ar++q+fapGipqvyy Glla  n
  lcl|FitnessBrowser__ANA3:7022815 309 NEKQIDNLVETIHGNSQGESLQATGAAASNVDLYQINCTYYDALGQNDLDYLMARAIQFFAPGIPQVYYTGLLAIPN 385
                                       ************9888877778889999************************************************* PP

                         TIGR03852 377 dielleetkeGrninrhyytleeiaeevkrpvvkkllkllkfrneseafdldgkievetkeeeeleivrenkdekek 453
                                       d+ ll++t +Gr+inr y ++e++++++++pvvk+l++l+k rn+s+af+  g++++   + ++l++++++  ++ +
  lcl|FitnessBrowser__ANA3:7022815 386 DMTLLNQTHVGRDINRPYLNREKVQQALQKPVVKALIQLIKLRNNSAAFN--GRFSMAA-SGKTLTLTWSA--QNAS 457
                                       *************************************************9..***9876.56789999998..5667 PP

                         TIGR03852 454 avlkanlktkk 464
                                       a l++++++k+
  lcl|FitnessBrowser__ANA3:7022815 458 ASLSLDFAHKQ 468
                                       88888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (470 nodes)
Target sequences:                          1  (494 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: 9.18
//
[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:

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