GapMind for catabolism of small carbon sources

 

Alignments 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.

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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