GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pedobacter sp. GW460-11-11-14-LB5

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate CA265_RS16605 CA265_RS16605 1-pyrroline-5-carboxylate dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>FitnessBrowser__Pedo557:CA265_RS16605
          Length = 544

 Score =  524 bits (1350), Expect = e-153
 Identities = 273/540 (50%), Positives = 358/540 (66%), Gaps = 7/540 (1%)

Query: 30  YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89
           + VP   NEP   YA G+ +R  L+EA+A   R+  L +P+ I G+EV + +      P 
Sbjct: 6   FNVPTPVNEPINSYAPGTKERSLLKEAIADA-RSKQLDIPMFIGGQEVHTKNKKKVVAPH 64

Query: 90  SHGPV-ATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148
            H  V AT+S      V+ AI++AL A+  W +  +  RA++F+KAADLI+TKYRY + A
Sbjct: 65  DHQHVLATFSYGDKSHVKQAIDAALAAKADWEALAWEHRAAIFMKAADLIATKYRYQINA 124

Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208
            TM GQ KNA+QAEID+A EL DF RF V Y +D+Y QQP     G+WNR E RPLEGF+
Sbjct: 125 ATMLGQSKNAYQAEIDAACELVDFLRFNVSYMQDIYGQQPPVSPNGMWNRTEQRPLEGFI 184

Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268
           +A++PFNFTAI GNL    A+MGNVVVWKP+ + + +  ++ QI  EAGLP  VI  +  
Sbjct: 185 FALTPFNFTAIAGNLPACVAMMGNVVVWKPADTQVYAANVIMQIFREAGLPDGVINLIFA 244

Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328
           +  EV   V +H DFA +HFTGST VF+ ++  I T +   KY+SYPRIVGETGGK+F L
Sbjct: 245 DGPEVGDVVFNHADFAGIHFTGSTKVFQEIWKTIGTNI--HKYKSYPRIVGETGGKDFIL 302

Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388
           +H SAD+  +A   VRGAFEYQGQKCSA SR Y+  S+     + +  +  S K+G   D
Sbjct: 303 VHPSADVAASATAIVRGAFEYQGQKCSAASRTYIPKSLWPEIKKLMIRDLASFKMGGTED 362

Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448
           F+NF   VI E SF KLAK ID+AK D  +E++AGG+YD SKG++I+PT+    +P +  
Sbjct: 363 FSNFINAVIDERSFDKLAKYIDQAKKDKGVEVIAGGNYDKSKGYFIEPTILVVDDPKYTT 422

Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508
           +  ELFGP+L VY Y D    +F ++ + ID T  Y LTG++ +QDR A+  A+  LRN+
Sbjct: 423 MCEELFGPVLSVYVYED---QEFDQVLEIIDTTSPYALTGAILSQDRYAIEKASYALRNS 479

Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568
           AGNFYIN K TGAVVGQQPFGGAR SGTNDKAG+   L R+VS R+IKE F P     YP
Sbjct: 480 AGNFYINDKCTGAVVGQQPFGGARGSGTNDKAGAMINLLRWVSPRTIKETFNPPTDYRYP 539


Lambda     K      H
   0.316    0.130    0.379 

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: 876
Number of extensions: 30
Number of successful extensions: 5
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: 572
Length of database: 544
Length adjustment: 36
Effective length of query: 536
Effective length of database: 508
Effective search space:   272288
Effective search space used:   272288
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 CA265_RS16605 CA265_RS16605 (1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.10951.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.4e-252  825.0   1.5   1.6e-252  824.8   1.5    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS16605  CA265_RS16605 1-pyrroline-5-carb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS16605  CA265_RS16605 1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  824.8   1.5  1.6e-252  1.6e-252       2     531 ..      13     540 ..      12     542 .. 0.99

  Alignments for each domain:
  == domain 1  score: 824.8 bits;  conditional E-value: 1.6e-252
                                  TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnatee 69 
                                                neP+++++pg+ker ll++++++++sk+l+iP+ igg+ev ++n + +vvaP+dhq++la++ + +++
  lcl|FitnessBrowser__Pedo557:CA265_RS16605  13 NEPINSYAPGTKERSLLKEAIADARSKQLDIPMFIGGQEVHTKN-KKKVVAPHDHQHVLATFSYGDKS 79 
                                                9**************************************99888.59********************* PP

                                  TIGR01236  70 dvkkaveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelid 137
                                                +vk+a++aal+ak +W++l +++raaif+kaadl+++kyr++i+aatmlgqsk+ yqaeida++el+d
  lcl|FitnessBrowser__Pedo557:CA265_RS16605  80 HVKQAIDAALAAKADWEALAWEHRAAIFMKAADLIATKYRYQINAATMLGQSKNAYQAEIDAACELVD 147
                                                ******************************************************************** PP

                                  TIGR01236 138 ffrfnvkyarelleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPs 205
                                                f+rfnv y +++++qqP vs +g +n++e rpleGf++a++Pfnftaia+nl+++ a+mGnvvvWkP+
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 148 FLRFNVSYMQDIYGQQPPVSPNGMWNRTEQRPLEGFIFALTPFNFTAIAGNLPACVAMMGNVVVWKPA 215
                                                *****************99************************************************* PP

                                  TIGR01236 206 ktavlsnyllmkileeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnld 273
                                                +t+v+++ ++m+i++eaGlP gvin++ adg +v+dvv  + d+a++hftGst+vf+e+wk++ +n++
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 216 DTQVYAANVIMQIFREAGLPDGVINLIFADGPEVGDVVFNHADFAGIHFTGSTKVFQEIWKTIGTNIH 283
                                                ******************************************************************** PP

                                  TIGR01236 274 kyrnfPrivGetGGkdfvlvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellae 341
                                                ky+++PrivGetGGkdf+lvhpsadv   ++a++rgafeyqGqkcsaasr y+pkslw+e+k+ ++++
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 284 KYKSYPRIVGETGGKDFILVHPSADVAASATAIVRGAFEYQGQKCSAASRTYIPKSLWPEIKKLMIRD 351
                                                ******************************************************************** PP

                                  TIGR01236 342 lkkvkvgdvddlssfmgavideksfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdP 409
                                                l++ k+g  +d+s+f+ avide+sf+k+ k+i++akkd   +e++aGG+yd+skGyf+ePt++  +dP
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 352 LASFKMGGTEDFSNFINAVIDERSFDKLAKYIDQAKKDK-GVEVIAGGNYDKSKGYFIEPTILVVDDP 418
                                                *************************************98.9*************************** PP

                                  TIGR01236 410 keklmkeeifGPvltvyvydddkykeilevvdstskyaltGavfakdreaieeaekklrfaaGnfyin 477
                                                k  +m ee+fGPvl+vyvy+d++++++le++d+ts yaltGa++++dr aie+a+ +lr++aGnfyin
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 419 KYTTMCEELFGPVLSVYVYEDQEFDQVLEIIDTTSPYALTGAILSQDRYAIEKASYALRNSAGNFYIN 486
                                                ******************************************************************** PP

                                  TIGR01236 478 dkstGavvgqqpfGGarlsGtndkaGapkillrfvsarsiketfkeltdfkypy 531
                                                dk+tGavvgqqpfGGar sGtndkaGa+ +llr+vs+r+iketf+++td++yp+
  lcl|FitnessBrowser__Pedo557:CA265_RS16605 487 DKCTGAVVGQQPFGGARGSGTNDKAGAMINLLRWVSPRTIKETFNPPTDYRYPF 540
                                                ****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (544 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: 00:00:00.02
# Mc/sec: 11.56
//
[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:

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:

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:

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:

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