Alignments for a candidate for scrP in Algiphilus aromaticivorans DG1253

GapMind for catabolism of small carbon sources

Alignments for a candidate for scrP in Algiphilus aromaticivorans DG1253

Align sucrose phosphorylase (LmSPase) (EC 2.4.1.7) (characterized)
to candidate WP_043766493.1 U743_RS06285 sucrose phosphorylase

Query= CAZy::BAA14344.1
         (490 letters)



>NCBI__GCF_000733765.1:WP_043766493.1
          Length = 480

 Score =  342 bits (878), Expect = 1e-98
 Identities = 186/467 (39%), Positives = 270/467 (57%), Gaps = 11/467 (2%)

Query: 1   MEIQNKAMLITYADSLGKNLKDVHQVLKEDIGDAIGGVHLLPFFPSTGDRGFAPADYTRV 60
           M ++N   LI Y D +G ++ D+H+V++E      GGVHLLP FPS  D GF+P  +  +
Sbjct: 1   MILRNLPHLIAYPDRMGSSISDLHKVMREHFPRCFGGVHLLPPFPSNADGGFSPLTHREI 60

Query: 61  DAAFGDWADVEALGEEYYLMFDFMINHISRESVMYQDFKKNHDDSKYKDFFIRWEKFWAK 120
           D  +G W +VEAL  EY L  D ++NHI+ ES  ++DF  N  DS+Y + F+  +     
Sbjct: 61  DPRYGSWEEVEALAAEYDLCLDLVLNHIADESPEFKDFLANGRDSRYAELFVDVDAL--- 117

Query: 121 AGENRPTQADVDLIYKRKDKAPTQEITFDDGTTENLWNTFGEEQIDIDVNSAIAKEFIKT 180
                 T  D+  I+ RK+K P +E+T  +G  + +W TF E+Q+D++ ++    +F++ 
Sbjct: 118 ---GEITSDDLAKIHIRKEKEPFREVTLANGEKKRVWCTFTEKQVDLNYDAEATYDFMEE 174

Query: 181 TLEDMVKHGANLIRLDAFAYAVKKVDTNDFFVEPEIWDTLNEVREILTPLKAEILPEIHE 240
            L  M  HG  L RLDAF Y  KK+ T+ F VEP+++D L         + AE+LPE+H+
Sbjct: 175 NLRVMTGHGVKLFRLDAFGYTTKKIGTSCFLVEPDVYDILGWFHRTANRMGAEVLPEVHD 234

Query: 241 HYSIPKKINDHGYFTYDFALPMTTLYTLYSGKTNQLAKWLKMSPMKQFTTLDTHDGIGVV 300
           H S    I   G   Y FALP   LY+L    +  L  WL++ P  Q T LDTHDGI + 
Sbjct: 235 HSSYQFAIGMRGMRPYGFALPPLLLYSLLDANSVHLKNWLRVCPRNQITVLDTHDGICIP 294

Query: 301 DARDILTDDEIDYASEQLYKVGANVKKTYSSASYNNLD-IYQINSTYYSALGNDDAAYLL 359
           D   IL  D+I    + + +  A+     S+A+ +++  IYQ+  T+Y AL  +D AY+ 
Sbjct: 295 DVEGILPADKIQAVIDNVSQRSADPILRRSAANVHSVGAIYQLTCTFYDALKQNDDAYIA 354

Query: 360 SRVFQVFAPGIPQIYYVGLLAGENDIALLESTKEGRNINRHYYTREEVKSEVKRPVVANL 419
           +R  Q+FAPGIPQIYYVGLLAG ND  L+E T E R+INR Y+  E V    ++PVV  L
Sbjct: 355 ARAIQLFAPGIPQIYYVGLLAGTNDEELMEHTGELRDINRTYFDLEAVAEATEKPVVRRL 414

Query: 420 LKLLSWRNESPAFDLAGSITVDTPTDTTIVVTRQDENGQNKAVLTAD 466
           ++LL +R   PAF   G+  +    DT+  V+ Q +NG  KA+L  D
Sbjct: 415 IQLLEFRCSHPAF--RGTFELVYSNDTS--VSMQWKNGDAKALLFVD 457


Lambda     K      H
   0.316    0.134    0.390 

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: 594
Number of extensions: 27
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: 490
Length of database: 480
Length adjustment: 34
Effective length of query: 456
Effective length of database: 446
Effective search space:   203376
Effective search space used:   203376
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: 52 (24.6 bits)

Align candidate WP_043766493.1 U743_RS06285 (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.2801205.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.2e-148  478.6   0.0   1.1e-147  478.3   0.0    1.0  1  NCBI__GCF_000733765.1:WP_043766493.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_043766493.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.3   0.0  1.1e-147  1.1e-147       5     466 ..       9     464 ..       5     468 .. 0.96

  Alignments for each domain:
  == domain 1  score: 478.3 bits;  conditional E-value: 1.1e-147
                             TIGR03852   5 lityadslGknlkelekvleeelkdavGGvhllpffpssgdrGfapsdyekvdeafGdwedvealsekyylmf 77 
                                           li+y+d +G+ + +l+kv+ e++  + GGvhllp fps +d Gf+p +++++d+++G+we+veal+ +y+l  
  NCBI__GCF_000733765.1:WP_043766493.1   9 LIAYPDRMGSSISDLHKVMREHFPRCFGGVHLLPPFPSNADGGFSPLTHREIDPRYGSWEEVEALAAEYDLCL 81 
                                           9************************************************************************ PP

                             TIGR03852  78 dfminhiskeseyykdflekkdeskykdlfirykdfwpegrpteedvdliykrkdrapyqevefadGstekvw 150
                                           d ++nhi+ es+ +kdfl++  +s+y++lf+  + +   g+ t +d+ +i+ rk++ p++ev++a+G++++vw
  NCBI__GCF_000733765.1:WP_043766493.1  82 DLVLNHIADESPEFKDFLANGRDSRYAELFVDVDAL---GEITSDDLAKIHIRKEKEPFREVTLANGEKKRVW 151
                                           *******************************99976...899******************************* PP

                             TIGR03852 151 ntfgeeqidldvtkevtkkfikenlenlaekGaslirldafayavkkldtndffvepeiwelldevrdilaak 223
                                           +tf e+q+dl+  +e t +f++enl+ ++ +G++l rldaf y++kk++t++f+vep+++++l   + +++ +
  NCBI__GCF_000733765.1:WP_043766493.1 152 CTFTEKQVDLNYDAEATYDFMEENLRVMTGHGVKLFRLDAFGYTTKKIGTSCFLVEPDVYDILGWFHRTANRM 224
                                           ************************************************************************* PP

                             TIGR03852 224 daeilpeihehytiqlkiaekdyyvydfalplvvlyslysgkterladwlkkspmkqfttldthdGiGvvdvk 296
                                           +ae+lpe+h+h ++q+ i  +++  y falp ++lysl  +++ +l++wl+ +p+ q t ldthdGi + dv+
  NCBI__GCF_000733765.1:WP_043766493.1 225 GAEVLPEVHDHSSYQFAIGMRGMRPYGFALPPLLLYSLLDANSVHLKNWLRVCPRNQITVLDTHDGICIPDVE 297
                                           ************************************************************************* PP

                             TIGR03852 297 dlltdeeidatkeelykvGanvkkiyssaeynnl.diyqinstyysalGdddkayllarvvqvfapGipqvyy 368
                                            +l+ ++i+a  +++ +  a+     s+a+ + +  iyq+ +t+y al ++d+ay+ ar++q+fapGipq+yy
  NCBI__GCF_000733765.1:WP_043766493.1 298 GILPADKIQAVIDNVSQRSADPILRRSAANVHSVgAIYQLTCTFYDALKQNDDAYIAARAIQLFAPGIPQIYY 370
                                           *******************99776667776666537************************************* PP

                             TIGR03852 369 vGllaGkndielleetkeGrninrhyytleeiaeevkrpvvkkllkllkfrneseafdldgkievetkeeeel 441
                                           vGllaG nd el+e+t e r+inr y++le +ae++++pvv++l++ll+fr ++ af   g++e+  ++++++
  NCBI__GCF_000733765.1:WP_043766493.1 371 VGLLAGTNDEELMEHTGELRDINRTYFDLEAVAEATEKPVVRRLIQLLEFRCSHPAFR--GTFELVYSNDTSV 441
                                           *********************************************************9..************* PP

                             TIGR03852 442 eivrenkdekekavlkanlktkkfk 466
                                           ++ ++n  ++ ka l ++l+ kk +
  NCBI__GCF_000733765.1:WP_043766493.1 442 SMQWKN--GDAKALLFVDLNFKKTT 464
                                           ****99..55566666666555544 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: 00:00:00.00
# Mc/sec: 24.41
//
[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 2024 update 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