Aligments for a candidate for pimF in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Shewanella loihica PV-4

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__PV4:5209977
          Length = 706

 Score =  370 bits (951), Expect = e-106
 Identities = 251/700 (35%), Positives = 363/700 (51%), Gaps = 33/700 (4%)

Query: 13  VAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGR-TFIAGADITEFG 69
           +A++T+D P   +N L A     I E +    AD  ++ +V++   + +F+AGADI+   
Sbjct: 14  IAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLD 73

Query: 70  KPPQPPAL-------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK-- 120
                          ++V  ALE+   P +AAI+G  LGGGLE+AL CH RV     K  
Sbjct: 74  ACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSNKTM 133

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAG 180
           LGLPEV+LGLLPG GGTQRLPR VG   ++ M++ G  + A +ALK GLV++VV   +  
Sbjct: 134 LGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPESILL 193

Query: 181 AVAFAKKVLAEKRPLRR--LRDDDSKLAAAKADRSI-FTNAVAAMTKKARG-LEAPFACA 236
             A  +  LA  RP ++  L   +  L      R+I F  A+  + KK +G   AP    
Sbjct: 194 QTAI-EMALAGARPAKKPKLSTVEKLLEGTPVGRNIIFEQALKQVNKKTQGNYPAPEKII 252

Query: 237 DAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVS 296
           D +   +     +GL+ E + F  LVVS++S+A R  FFA  E  K  G  D   P+ V+
Sbjct: 253 DCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTEMKKESGAGD-VSPKAVN 311

Query: 297 RVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA 355
           +V ++G G MGGGIA ++   A IPV + +  E  L   L    K       R  + P  
Sbjct: 312 KVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAYKLLAKGVKRRHMTPAV 371

Query: 356 PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSI 415
               MAL+T     + +KDAD+++EAVFE + +K ++   V+       + ASNTS L I
Sbjct: 372 RDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERECGEHTIFASNTSSLPI 431

Query: 416 DEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGV 475
            +IA   +RP++V+G+H+FSP   M L E++   KT+P  + T V+ A+K  K P+VV  
Sbjct: 432 KQIAEAAERPENVIGLHYFSPVEKMPLVEVIAHDKTSPQTIATTVAFARKQGKTPIVVKD 491

Query: 476 CDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWR--- 532
             GF  NR+LA    ++  LL EG     +D  + KFG P+GP  + D  G+D+G +   
Sbjct: 492 GAGFYVNRILALYMNEAANLLLEGQSVDHLDKALVKFGFPVGPMTLLDEVGIDVGAKISP 551

Query: 533 -SRKDRG--IKSEIA-DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKL 588
              K+ G   K+  A D L    R G+K GKG+Y+Y   S+  + D  V  ++  T    
Sbjct: 552 ILEKELGERFKAPAAFDKLLADDRKGRKNGKGFYQYGAKSKKKLVDESVYGVLGLT---- 607

Query: 589 GLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYA 648
                D     + ER V  M+NE  R LEE I A P D D+  ++G G+P + GGP  Y 
Sbjct: 608 --PGADGEPIALAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPPFLGGPFRYM 665

Query: 649 DSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           DS+G KH+ E L  Y     D    P   L  +A  G  F
Sbjct: 666 DSLGAKHLVETLKRYQDQFGD-RFAPCDRLVEMAESGSKF 704


Lambda     K      H
   0.317    0.134    0.383 

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: 1047
Number of extensions: 55
Number of successful extensions: 6
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: 699
Length of database: 706
Length adjustment: 39
Effective length of query: 660
Effective length of database: 667
Effective search space:   440220
Effective search space used:   440220
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 (21.7 bits)
S2: 54 (25.4 bits)

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

Downloads

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

Related tools

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, or view the source code.

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