Alignments for a candidate for paaH in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Azospirillum lipoferum B510

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012976491.1 AZL_RS21100 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000010725.1:WP_012976491.1
          Length = 728

 Score =  572 bits (1473), Expect = e-167
 Identities = 330/703 (46%), Positives = 432/703 (61%), Gaps = 19/703 (2%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           V ++T+DH PVNAL+  +R  L AA+ AA  D +V A+++ GAGR F  G DI EF  P 
Sbjct: 23  VAVITLDHPPVNALALALRTRLGAALHAALRDVSVRAIVLAGAGRGFCGGGDITEFDLPA 82

Query: 78  V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
           V   P+   + + IE   KPVVAA+HG ALGGGLE+ALA H R+A    ++GLPEV LGL
Sbjct: 83  VCQEPTPATLFSLIENSPKPVVAALHGMALGGGLELALACHARVAEARTQVGLPEVHLGL 142

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE---GLAYV 192
           +PGAGGTQR PRL+G + AL+LI+ GR   A+     GL DRL     + A     +A  
Sbjct: 143 VPGAGGTQRLPRLVGFELALNLIVQGRTQPAQSLRDSGLFDRLTDGSPVEAAVEVAMALA 202

Query: 193 HELLAAHAPVRRTRDAAALSDRAASLAAV-ATARAETAKKSRGLFSPLKIVDAVEAAIEQ 251
            EL   +A     R   AL+ R A+  A  A ARA    + RGL +P+  VD VE A   
Sbjct: 203 GELAVPNAADGMLRRTGALTPRLANAQAFFAFARATVQSRFRGLPAPVACVDCVEKAATL 262

Query: 252 PFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAA----KPRTLNTIGVVG 307
           PF EGL  E   F     + + AGL HAF AER   +A + R      KPR + T+ V+G
Sbjct: 263 PFHEGLAFEHDCFTRLRGTAEFAGLRHAFLAER---RAADIRGLPDGIKPRPVKTVAVIG 319

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
            GTMG GIA+++ +AGL VT+IER+  +L RG A I +  +  + KGRL+AE+ A  +  
Sbjct: 320 AGTMGGGIAMSLANAGLAVTLIEREQEALDRGLAIIRQTCESALRKGRLTAEEAAGRLDL 379

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
             G   YD +  ADLVIEAVFEDL VK+ VF ++D V +AG VLATNTS LD+D +A   
Sbjct: 380 IKGCVGYDPVRQADLVIEAVFEDLEVKRQVFEQIDAVARAGTVLATNTSMLDLDRIAGFT 439

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
            RP DV+GLHFFSPA++MKLLEVV     + DV+ATA  LA+++ KT V +GVC+GFIGN
Sbjct: 440 RRPQDVLGLHFFSPAHVMKLLEVVRGAATAPDVLATAIALARRIGKTSVVSGVCEGFIGN 499

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547
           R+L  Y   A  ++++GA P+Q+D A+  +G  MGPF+V DLAG D+G   R +  A R 
Sbjct: 500 RILQPYLYQAGRLLDEGALPHQVDQAIERWGMAMGPFRVSDLAGNDLGAGIRAQVMANR- 558

Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607
           P   +    D +   G FGQKSGRG+Y Y    R   P  EV A + AE  R G+  R+ 
Sbjct: 559 PELAFSGSFDAVVAMGRFGQKSGRGWYDYSASQRGPQPSMEVNAAVVAESGRLGLRRRTI 618

Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667
            DEEII R + A++NEGA V+ + IA R  D+DV +  GYGFPR+RGGPM  AD  GL  
Sbjct: 619 ADEEIIDRLLLALVNEGAKVLGDGIAQRASDIDVVYTAGYGFPRWRGGPMFAADRRGLAD 678

Query: 668 ILADIREFAK-----EDPLFWKPSPLLIELVERGADFASLNQS 705
           IL  +R FA+     +D  FW+P+PLL  L +RG  F +   S
Sbjct: 679 ILGTMRRFAEAAPDPQDASFWQPAPLLRRLADRGRSFGTFVDS 721


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: 1236
Number of extensions: 61
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: 706
Length of database: 728
Length adjustment: 40
Effective length of query: 666
Effective length of database: 688
Effective search space:   458208
Effective search space used:   458208
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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
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