GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas stutzeri RCH2

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>FitnessBrowser__psRCH2:GFF4162
          Length = 701

 Score =  652 bits (1683), Expect = 0.0
 Identities = 336/693 (48%), Positives = 467/693 (67%), Gaps = 2/693 (0%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           DVV  E++G++ L+T+++ PVNAL   VR GL  A ++A+AD  V AV +V  G  FIAG
Sbjct: 3   DVVRLEVQGEIALITVNNPPVNALGQAVREGLQKAFQSAEADPQVRAVALVCEGNTFIAG 62

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADI+EFGKPP  PSLP+V   IEAC K  VA IHG ALGGGLEVAL  HYRIA   AK+G
Sbjct: 63  ADIKEFGKPPQAPSLPEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYRIARKDAKVG 122

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPEV+LGLLPGAGGTQR PRL G + AL++I+SG+  SA EA+   ++D L   D ++  
Sbjct: 123 LPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDELFEGD-LVEA 181

Query: 188 GLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247
           GLAYV  ++      RRT +     + A + A +    AE AK+  GLFSPL+ + AVEA
Sbjct: 182 GLAYVRRMVEEGRTPRRTGEQTQGLEGADNEALIRAKHAEVAKRMPGLFSPLRCIAAVEA 241

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVV 306
           A + P  EGL+ ER+LF EC++SPQR  L+H+FFAER+  K  +  +  KPR++N+  V+
Sbjct: 242 ATKLPLAEGLKRERELFAECLNSPQRGALVHSFFAERQAGKINDLPSDTKPRSINSAAVI 301

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           GGGTMG GIA++  +AG+PV ++E ++ +L RG       Y   + +G L+ +     ++
Sbjct: 302 GGGTMGVGIALSFANAGVPVKLLEINEEALQRGLQRARDTYAASVKRGSLTEDAMEQRLA 361

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
              G T Y ALA AD+V+EAVFE++ VKQ VF +LD +CK GA+LA+NTS LD+DA+A+ 
Sbjct: 362 LIEGVTEYAALADADVVVEAVFEEMGVKQQVFEQLDAICKPGAILASNTSSLDLDAIAAF 421

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
             RP DV+GLHFFSPAN+M+LLEVV   + S +V+ATA  + K+L+K  V  GVCDGF+G
Sbjct: 422 TKRPEDVVGLHFFSPANVMRLLEVVRGAKTSDEVLATAMAIGKQLKKVSVVVGVCDGFVG 481

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR++  Y   A+ ++E+GA+P Q+DAA+R FG  MGPF + DL+G DIG A RKR+ AT 
Sbjct: 482 NRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRATL 541

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
                +  ++D+LC  G  GQK+G G+Y Y  G+R+   +P++  +++A     GI  ++
Sbjct: 542 PAHLDFPTVSDKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASLEKGIERKA 601

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
             ++ I+ R + A++NEGA ++ E IA R  D+DV +L GYGFP +RGGPM YAD VGL 
Sbjct: 602 LDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMFYADSVGLD 661

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADF 699
           ++LA ++E       +WKP+PLL +L   G  F
Sbjct: 662 RVLARVKELHARCGDWWKPAPLLEKLAAEGRTF 694


Lambda     K      H
   0.320    0.136    0.392 

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: 1145
Number of extensions: 35
Number of successful extensions: 3
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: 706
Length of database: 701
Length adjustment: 39
Effective length of query: 667
Effective length of database: 662
Effective search space:   441554
Effective search space used:   441554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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