Alignments for a candidate for fucI in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucI in Bacteroides thetaiotaomicron VPI-5482

Align L-fucose isomerase (EC 5.3.1.25); D-arabinose isomerase (EC 5.3.1.3) (characterized)
to candidate 350801 BT1273 L-fucose isomerase (NCBI ptt file)

Query= BRENDA::C0SSE7
         (595 letters)



>FitnessBrowser__Btheta:350801
          Length = 591

 Score =  834 bits (2155), Expect = 0.0
 Identities = 405/588 (68%), Positives = 477/588 (81%), Gaps = 5/588 (0%)

Query: 12  PKIGIRPTIDGRRKGVRESLEETTMNMAKAVAKLLEENVFYYNGQPVECVIADTCIGGVK 71
           PKIGIRPTIDGR+ GVRESLEE TMN+AKAVA+L+  N+   +G PVEC+IAD  IG V 
Sbjct: 5   PKIGIRPTIDGRQGGVRESLEEKTMNLAKAVAELISNNLKNGDGSPVECIIADNTIGRVA 64

Query: 72  EAAEAAEKFAREGVGVSITVTPCWCYGTETMDMDPHIPKAVWGFNGTERPGAVYLAAVLA 131
           E+A  AEKF REGVG +ITVT CWCYG ETMDM+PH PKAVWGFNGTERPGAVYLAAVLA
Sbjct: 65  ESAACAEKFEREGVGSTITVTSCWCYGAETMDMNPHYPKAVWGFNGTERPGAVYLAAVLA 124

Query: 132 GYNQKGLPAFGIYGKDVQDAGDTNIPEDVKEKLIRFAKAGLAVAMMKGKSYLSIGSVSMG 191
           G+ QKGLPAFGIYG+DVQD  D  IPEDV EK++RFA+A  AVA M+GKSYLS+GSVSMG
Sbjct: 125 GHAQKGLPAFGIYGRDVQDLDDNTIPEDVAEKILRFARAAQAVATMRGKSYLSMGSVSMG 184

Query: 192 IAGSVVQEDFFQNYLGMRNEYVDMSEFVRRIELEIYDKEEYERALKWVKENCKV--GPD- 248
           IAGS+V  DFFQ YLGMRNE +D++E +RR+E  IYD EEY +A+ W ++ CKV  G D 
Sbjct: 185 IAGSIVNPDFFQEYLGMRNESIDLTEIIRRMEEGIYDHEEYAKAMAWTEKYCKVNEGEDF 244

Query: 249 NNRDGFKRTEEQKEKDWEISVKMALIARDLMVGNKKLEEMGYGEEALGRNAIVAGFQGQR 308
            NR   ++  EQK+ DWE  VKM +I RDLM GN KL+EMG+ EEALG NAI AGFQGQR
Sbjct: 245 KNRPEKRKKREQKDADWEFVVKMMIIMRDLMTGNPKLKEMGFKEEALGHNAIAAGFQGQR 304

Query: 309 QWTDYFPNGDFMETILNSSFDWNGKRAPYIFATENDNLNGISMLFGYLLTNTAQIFADVR 368
           QWTD++PNGD+ E +LN+SFDWNG R  ++ ATEND  NG++MLFG+LLTN AQIF+DVR
Sbjct: 305 QWTDFYPNGDYPEALLNTSFDWNGIREAFVVATENDACNGVAMLFGHLLTNRAQIFSDVR 364

Query: 369 TYWSPEAVKRVTGYTLEGRAANGIIHLINSGAAALDGTGEQ-TKDGKPVIKPYYELTDED 427
           TYWSPEAVKRVTG  L G AANGIIHLINSGA  LDG+G+    +G PV+K  + LTD D
Sbjct: 365 TYWSPEAVKRVTGKELTGLAANGIIHLINSGATTLDGSGQSLDAEGNPVMKEPWNLTDAD 424

Query: 428 IKKCLEATQFRPASTEYFRGGGYSTDFLTKGGMPVTISRLNIVKGLGPVLQIAEGYTVDL 487
           ++ CL+AT + PA  +YFRGGG+S++FL+KGGMPVT+ RLN++KGLGPVLQIAEG+TV++
Sbjct: 425 VENCLKATTWYPADRDYFRGGGFSSNFLSKGGMPVTMMRLNLIKGLGPVLQIAEGWTVEI 484

Query: 488 PEEVHDVLDKRTDPTWPTTWFVPNLTGEGAFKDVYSVMNNWGANHCSISYGHIGADLITL 547
             E+H  L+ RTDPTWPTTWFVP L  + AFKDVYSVMNNWGANH +ISYGHIG DLITL
Sbjct: 485 DPEIHQKLNMRTDPTWPTTWFVPRLCDKSAFKDVYSVMNNWGANHGAISYGHIGQDLITL 544

Query: 548 ASILRIPVNMHNVPEEKIFRPDAWSMFGTKDLEGADYRACKNFGPIYK 595
           AS+LRIPV MHNV E +IFRP AW+ FG  D EGADYRAC  +GPIYK
Sbjct: 545 ASMLRIPVCMHNVDENEIFRPTAWNAFG-MDKEGADYRACTTYGPIYK 591


Lambda     K      H
   0.317    0.137    0.415 

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: 1156
Number of extensions: 40
Number of successful extensions: 4
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: 595
Length of database: 591
Length adjustment: 37
Effective length of query: 558
Effective length of database: 554
Effective search space:   309132
Effective search space used:   309132
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 350801 BT1273 (L-fucose isomerase (NCBI ptt file))
to HMM TIGR01089 (fucI: L-fucose isomerase (EC 5.3.1.25))

# 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/TIGR01089.hmm
# target sequence database:        /tmp/gapView.12059.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01089  [M=587]
Accession:   TIGR01089
Description: fucI: L-fucose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
          0 1243.2   0.9          0 1243.0   0.9    1.0  1  lcl|FitnessBrowser__Btheta:350801  BT1273 L-fucose isomerase (NCBI 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350801  BT1273 L-fucose isomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1243.0   0.9         0         0       1     587 []       2     591 .]       2     591 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1243.0 bits;  conditional E-value: 0
                          TIGR01089   1 kklpkigirptidgrrmgvresleektlnlakavaellseklrhadgaavecviadstiggvaeaaacaekferen 76 
                                        kk+pkigirptidgr++gvresleekt+nlakavael+s++l+++dg++vec+iad+tig+vae+aacaekfere+
  lcl|FitnessBrowser__Btheta:350801   2 KKYPKIGIRPTIDGRQGGVRESLEEKTMNLAKAVAELISNNLKNGDGSPVECIIADNTIGRVAESAACAEKFEREG 77 
                                        68************************************************************************** PP

                          TIGR01089  77 vgltitvtscwcygsetidmdphrpkaiwgfngterpgavylaaalaghsqkglpafsiygrdvqdaddtsipedv 152
                                        vg+titvtscwcyg+et+dm+ph+pka+wgfngterpgavylaa+lagh+qkglpaf+iygrdvqd+dd++ipedv
  lcl|FitnessBrowser__Btheta:350801  78 VGSTITVTSCWCYGAETMDMNPHYPKAVWGFNGTERPGAVYLAAVLAGHAQKGLPAFGIYGRDVQDLDDNTIPEDV 153
                                        **************************************************************************** PP

                          TIGR01089 153 eekllrfaraglavaslrgksylslgsvsmgiagsivnkdffqeylgmrneavdlteikrrldekiydeeelelal 228
                                        +ek+lrfara++ava++rgksyls+gsvsmgiagsivn+dffqeylgmrne++dltei+rr++e+iyd+ee+++a+
  lcl|FitnessBrowser__Btheta:350801 154 AEKILRFARAAQAVATMRGKSYLSMGSVSMGIAGSIVNPDFFQEYLGMRNESIDLTEIIRRMEEGIYDHEEYAKAM 229
                                        **************************************************************************** PP

                          TIGR01089 229 awvekyckvgede...nskekqrnaeqkaavleevvkmaiiirdlmvgnpklaelgfaeealgynaiaagfqgqrh 301
                                        aw+ekyckv+e+e   n++ek++++eqk+a++e+vvkm+ii+rdlm+gnpkl+e+gf+eealg+naiaagfqgqr+
  lcl|FitnessBrowser__Btheta:350801 230 AWTEKYCKVNEGEdfkNRPEKRKKREQKDADWEFVVKMMIIMRDLMTGNPKLKEMGFKEEALGHNAIAAGFQGQRQ 305
                                        ***********99899************************************************************ PP

                          TIGR01089 302 wtdqypngdfaeallnssfdwngvreafvvatendslngvamllghqltgkaqifadvrtywspeavervtgkkle 377
                                        wtd+ypngd++ealln+sfdwng+reafvvatend++ngvaml+gh+lt++aqif+dvrtywspeav+rvtgk+l+
  lcl|FitnessBrowser__Btheta:350801 306 WTDFYPNGDYPEALLNTSFDWNGIREAFVVATENDACNGVAMLFGHLLTNRAQIFSDVRTYWSPEAVKRVTGKELT 381
                                        **************************************************************************** PP

                          TIGR01089 378 glaengiihlinsgsaaldgsgksrdaegnptlkeawelteeeaeaclkatewcpavreyfrggglssrfltkggv 453
                                        gla+ngiihlinsg+++ldgsg+s daegnp++ke+w+lt++++e+clkat+w+pa+r+yfrggg+ss+fl+kgg+
  lcl|FitnessBrowser__Btheta:350801 382 GLAANGIIHLINSGATTLDGSGQSLDAEGNPVMKEPWNLTDADVENCLKATTWYPADRDYFRGGGFSSNFLSKGGM 457
                                        **************************************************************************** PP

                          TIGR01089 454 pvtltrvnlikglgpvlqiaegwsveldkdvhdklnkrtnetwpttwfvprltgkgaftdvysvmanwganhgvlt 529
                                        pvt++r+nlikglgpvlqiaegw+ve+d+++h+kln+rt++twpttwfvprl++k+af+dvysvm+nwganhg+++
  lcl|FitnessBrowser__Btheta:350801 458 PVTMMRLNLIKGLGPVLQIAEGWTVEIDPEIHQKLNMRTDPTWPTTWFVPRLCDKSAFKDVYSVMNNWGANHGAIS 533
                                        **************************************************************************** PP

                          TIGR01089 530 yghvgadlitlasmlripvcmhnveekeifrpsawnafgmdkegqdyracqnygplyk 587
                                        ygh+g+dlitlasmlripvcmhnv+e+eifrp+awnafgmdkeg+dyrac++ygp+yk
  lcl|FitnessBrowser__Btheta:350801 534 YGHIGQDLITLASMLRIPVCMHNVDENEIFRPTAWNAFGMDKEGADYRACTTYGPIYK 591
                                        *********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (587 nodes)
Target sequences:                          1  (591 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: 00:00:00.03
# Mc/sec: 11.00
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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