Alignments for a candidate for scrP in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for scrP in Marinobacter adhaerens HP15

Align sucrose phosphorylase (LaSP;GtfA2;LBA1437) (EC 2.4.1.7) (characterized)
to candidate GFF2909 HP15_2853 sucrose phosphorylase

Query= CAZy::AAO21868.1
         (480 letters)



>FitnessBrowser__Marino:GFF2909
          Length = 480

 Score =  372 bits (956), Expect = e-107
 Identities = 192/454 (42%), Positives = 276/454 (60%), Gaps = 6/454 (1%)

Query: 1   MPIENKVMLITYPDSLGKNLKELDEILSEDLKGAVGGIHLLPFFPSTGDRGFAPTGYTEV 60
           M ++N V LI YPD +G NLK+L  ++   L  A+GG+H+LPFFPS  D GF+P  + EV
Sbjct: 1   MLLKNAVQLICYPDRIGNNLKDLYTVVDTHLSEAIGGLHILPFFPSNADGGFSPLTHKEV 60

Query: 61  DPKFGDWSDIEKIGKKYYLMFDFMINHISRQSKFYKDFKQKKDKSKYADLFLSWDKFWPE 120
           DPK G W DIE    KY L  D  +NHIS +S  + DF      S+YADLF+  DKF   
Sbjct: 61  DPKVGTWDDIEAFTAKYDLCVDLTVNHISDESPEFTDFIANGFDSEYADLFVHVDKF--- 117

Query: 121 GRPTRKDIDLIYKRKDRAPYQEITFTDGSKEKLWNTFGEEQIDMDVRKEVTQKFIKDTLR 180
           G  +  D+  I+ RK++ P++E+T +DG+K ++W TF E+QID++   ++  + ++  + 
Sbjct: 118 GEISPDDMAKIHIRKEKEPFREVTLSDGTKTRVWCTFTEQQIDLNYESDLAYQLMESYIG 177

Query: 181 ALIDHGADIIRLDAFAYAVKKLDTNDFFVEPEIWDLLKQVQDDISDKGAMILPEIHEHYS 240
            L   G +++RLDAF Y  K++ T+ F VEPE++ +L  V       GA  LPE+H+H S
Sbjct: 178 FLTSKGVNLLRLDAFGYTTKRIGTSCFLVEPEVYQILDWVNQVALKHGAECLPEVHDHTS 237

Query: 241 MPFKISKHGYYIYDFALPMVTLYSLYSGKSNRLADWLKKCPMKQFTTLDTHDGIGVVDAR 300
             + IS+   + Y FALP + LYSL    S  L +WL+ CP    T LDTHDGI + D  
Sbjct: 238 YQYAISRRNMHPYGFALPPLLLYSLLDANSTYLKNWLRMCPRNMVTVLDTHDGICIPDVE 297

Query: 301 DILSPDEIKYTSNELYKVGANVKKKYSSAEYHNLD-IYQINTTYYSALGNDDKKYFIARL 359
            +L  ++IK   + +    A+   + S+A  H++  IYQ+  T+Y AL  +D  Y  AR 
Sbjct: 298 GVLPDEKIKVLIDNIDARSADPIMRRSAANIHSVGAIYQLTCTFYDALMQNDDAYIAARA 357

Query: 360 IQMFAPGIPQVYYVGMLAGKNDIELLEKTKEGRNINRHYYGREEVAEETKRPLVAALLKL 419
           IQ F PGIPQVYYVG+LAG ND EL+E++ E R+INRHYY  EEV ++ ++P+V  LL L
Sbjct: 358 IQFFTPGIPQVYYVGLLAGCNDHELMEQSGELRDINRHYYTLEEVEQDIQKPVVQRLLSL 417

Query: 420 FNFRNNEAAFDLDGSIEITTPNENVIQITRMNKD 453
             FR+N  AF  DG  E+   N + + +   + D
Sbjct: 418 MKFRSNYPAF--DGHFELNYSNNSSVAMAWRHGD 449


Lambda     K      H
   0.319    0.138    0.407 

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: 644
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF2909 HP15_2853 (sucrose phosphorylase)
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.9944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.5e-156  506.4   0.3   4.2e-156  506.1   0.3    1.0  1  lcl|FitnessBrowser__Marino:GFF2909  HP15_2853 sucrose phosphorylase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2909  HP15_2853 sucrose phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.1   0.3  4.2e-156  4.2e-156       1     468 [.       5     466 ..       5     469 .. 0.96

  Alignments for each domain:
  == domain 1  score: 506.1 bits;  conditional E-value: 4.2e-156
                           TIGR03852   1 nkvmlityadslGknlkelekvleeelkdavGGvhllpffpssgdrGfapsdyekvdeafGdwedvealsekyyl 75 
                                         n v li y+d +G+nlk+l +v++++l++a+GG+h+lpffps +d Gf+p ++++vd+++G w+d+ea++ ky+l
  lcl|FitnessBrowser__Marino:GFF2909   5 NAVQLICYPDRIGNNLKDLYTVVDTHLSEAIGGLHILPFFPSNADGGFSPLTHKEVDPKVGTWDDIEAFTAKYDL 79 
                                         6789*********************************************************************** PP

                           TIGR03852  76 mfdfminhiskeseyykdflekkdeskykdlfirykdfwpegrpteedvdliykrkdrapyqevefadGstekvw 150
                                           d  +nhis es+ + df ++  +s+y+dlf++ ++f   g+ + +d+ +i+ rk++ p++ev+++dG++++vw
  lcl|FitnessBrowser__Marino:GFF2909  80 CVDLTVNHISDESPEFTDFIANGFDSEYADLFVHVDKF---GEISPDDMAKIHIRKEKEPFREVTLSDGTKTRVW 151
                                         *************************************9...5667799*************************** PP

                           TIGR03852 151 ntfgeeqidldvtkevtkkfikenlenlaekGaslirldafayavkkldtndffvepeiwelldevrdilaakda 225
                                         +tf e+qidl+ +++ + +++++ +  l++kG++l+rldaf y++k+++t++f+vepe++++ld v++++ +++a
  lcl|FitnessBrowser__Marino:GFF2909 152 CTFTEQQIDLNYESDLAYQLMESYIGFLTSKGVNLLRLDAFGYTTKRIGTSCFLVEPEVYQILDWVNQVALKHGA 226
                                         *************************************************************************** PP

                           TIGR03852 226 eilpeihehytiqlkiaekdyyvydfalplvvlyslysgkterladwlkkspmkqfttldthdGiGvvdvkdllt 300
                                         e lpe+h+h ++q  i+ ++++ y falp ++lysl  +++ +l++wl+++p+   t ldthdGi + dv+ +l+
  lcl|FitnessBrowser__Marino:GFF2909 227 ECLPEVHDHTSYQYAISRRNMHPYGFALPPLLLYSLLDANSTYLKNWLRMCPRNMVTVLDTHDGICIPDVEGVLP 301
                                         *************************************************************************** PP

                           TIGR03852 301 deeidatkeelykvGanvkkiyssaeynnl.diyqinstyysalGdddkayllarvvqvfapGipqvyyvGllaG 374
                                         de+i++  +++ +  a+     s+a+ + +  iyq+ +t+y al ++d+ay+ ar++q+f+pGipqvyyvGllaG
  lcl|FitnessBrowser__Marino:GFF2909 302 DEKIKVLIDNIDARSADPIMRRSAANIHSVgAIYQLTCTFYDALMQNDDAYIAARAIQFFTPGIPQVYYVGLLAG 376
                                         **************999777777777776637******************************************* PP

                           TIGR03852 375 kndielleetkeGrninrhyytleeiaeevkrpvvkkllkllkfrneseafdldgkievetkeeeeleivrenkd 449
                                          nd el+e++ e r+inrhyytlee+++++++pvv++ll l+kfr ++ afd  g++e++ ++++++ + +++ d
  lcl|FitnessBrowser__Marino:GFF2909 377 CNDHELMEQSGELRDINRHYYTLEEVEQDIQKPVVQRLLSLMKFRSNYPAFD--GHFELNYSNNSSVAMAWRHGD 449
                                         ***************************************************9..****************99955 PP

                           TIGR03852 450 ekekavlkanlktkkfkit 468
                                              +l ++l+ k+ k+t
  lcl|FitnessBrowser__Marino:GFF2909 450 --YYCHLFVDLNFKTVKVT 466
                                         ..55555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (470 nodes)
Target sequences:                          1  (480 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: 12.26
//
[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