Alignments for a candidate for galE in Allochromatium vinosum DSM 180

GapMind for catabolism of small carbon sources

Alignments for a candidate for galE in Allochromatium vinosum DSM 180

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_012970856.1 ALVIN_RS08175 UDP-glucose 4-epimerase GalE

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>NCBI__GCF_000025485.1:WP_012970856.1
          Length = 335

 Score =  470 bits (1209), Expect = e-137
 Identities = 221/335 (65%), Positives = 267/335 (79%)

Query: 1   MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60
           M +LVTGGAGYIGSHTC+ELL +G  +VV+DNL NS  E+L RV EITG+ + F+E DL 
Sbjct: 1   MRVLVTGGAGYIGSHTCLELLQAGIHVVVIDNLCNSREESLRRVGEITGQAVGFFEVDLR 60

Query: 61  DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120
           DREA+  +F++   +AVIHFAGLKAVGESVA PL+YY NN+ GT  LC+ M + GV+ +V
Sbjct: 61  DREALGEIFSQGRFDAVIHFAGLKAVGESVAQPLEYYDNNVQGTLTLCQVMAEAGVRNLV 120

Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180
           FSSSATVYG P + PI EDFP+GATNPYG++KL +E+IL DLH +D  W++ALLRYFNP 
Sbjct: 121 FSSSATVYGDPTSVPIREDFPVGATNPYGRSKLFIEEILHDLHVSDPRWNIALLRYFNPV 180

Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240
           GAH SGRIGEDPNGIPNNLMPY+AQVAVG+L++L VFGNDYPT DGTGVRDYIHVVDLA 
Sbjct: 181 GAHESGRIGEDPNGIPNNLMPYIAQVAVGRLQRLRVFGNDYPTPDGTGVRDYIHVVDLAR 240

Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300
           GH+ AL K+  S G   YNLGTG GYSVLE++ AFE+ SG+ VPY   +RR GDIA C+A
Sbjct: 241 GHLAALHKLQESPGVVTYNLGTGRGYSVLEVIAAFERASGRAVPYDIVERRSGDIACCYA 300

Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           DP+ A+ ELGW A+  LE M  D+WRWQS N +GY
Sbjct: 301 DPSLARDELGWSAEYDLERMVVDAWRWQSQNPDGY 335


Lambda     K      H
   0.315    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: 439
Number of extensions: 9
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: 339
Length of database: 335
Length adjustment: 28
Effective length of query: 311
Effective length of database: 307
Effective search space:    95477
Effective search space used:    95477
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: 49 (23.5 bits)

Align candidate WP_012970856.1 ALVIN_RS08175 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.28795.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-147  475.0   0.0   5.5e-147  474.9   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970856.1  ALVIN_RS08175 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970856.1  ALVIN_RS08175 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.9   0.0  5.5e-147  5.5e-147       1     331 [.       2     334 ..       2     335 .] 0.99

  Alignments for each domain:
  == domain 1  score: 474.9 bits;  conditional E-value: 5.5e-147
                                 TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 
                                               ++LvtGgaGyiGsh++ +ll++g +vvv+Dnl+++ +e+l+++ +it  +v ++e dl+d+e+l ++++
  lcl|NCBI__GCF_000025485.1:WP_012970856.1   2 RVLVTGGAGYIGSHTCLELLQAGIHVVVIDNLCNSREESLRRVGEITgqAVGFFEVDLRDREALGEIFS 70 
                                               69********************************************9999******************* PP

                                 TIGR01179  68 eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEe 136
                                               + ++daviHfa+l+avgEsv++Pl+YY+nnv++tl+L+++m++agv++l+Fsssa+vYg++++vpi E+
  lcl|NCBI__GCF_000025485.1:WP_012970856.1  71 QGRFDAVIHFAGLKAVGESVAQPLEYYDNNVQGTLTLCQVMAEAGVRNLVFSSSATVYGDPTSVPIRED 139
                                               ********************************************************************* PP

                                 TIGR01179 137 splnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevav 204
                                               +p++++npYGrskl +E+il+dl+ +d+++++++LRYFn++GA+e+g+iGe++++++ +l++++a+vav
  lcl|NCBI__GCF_000025485.1:WP_012970856.1 140 FPVGATNPYGRSKLFIEEILHDLHVSDPRWNIALLRYFNPVGAHESGRIGEDPNGIPnNLMPYIAQVAV 208
                                               *********************************************************9*********** PP

                                 TIGR01179 205 gkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkk 273
                                               g++++l++fG+dypt+DGt+vRDyiHv Dla +Hlaal++l+e+ ++ +ynlG+g+g+sv+evi a+++
  lcl|NCBI__GCF_000025485.1:WP_012970856.1 209 GRLQRLRVFGNDYPTPDGTGVRDYIHVVDLARGHLAALHKLQESPGVVTYNLGTGRGYSVLEVIAAFER 277
                                               ********************************************************************* PP

                                 TIGR01179 274 vsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                               +sg+ +++ + +rR+GD+a+++ad+s +++elgw+++yd Le ++ +aw+W++++++g
  lcl|NCBI__GCF_000025485.1:WP_012970856.1 278 ASGRAVPYDIVERRSGDIACCYADPSLARDELGWSAEYD-LERMVVDAWRWQSQNPDG 334
                                               ***************************************.**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (335 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.34
//
[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 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