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

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.21981.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.66
//
[ok]

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

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Protein sequences (fasta format)
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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