Alignments for a candidate for ech in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Azospirillum lipoferum B510

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_012976515.1 AZL_RS21225 fatty acid oxidation complex subunit alpha FadB

Query= metacyc::MONOMER-17591
         (715 letters)



>NCBI__GCF_000010725.1:WP_012976515.1
          Length = 727

 Score =  701 bits (1808), Expect = 0.0
 Identities = 361/711 (50%), Positives = 482/711 (67%), Gaps = 3/711 (0%)

Query: 1   MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60
           +++QG  + +  L  G+ EL FD  GESVNK +RL L EL  A+  ++ D +V G+++TS
Sbjct: 6   LMFQGNTLQLHALGDGLAELRFDRAGESVNKLDRLALDELNRALCLVREDRTVTGLLITS 65

Query: 61  GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120
           GKD FIVGADI EF D F + ++E+   N   + + +   DL VPTV A+NG+ALGGGLE
Sbjct: 66  GKDSFIVGADIFEFTDLFGMAEDEIAIHNAGQSAVITALADLPVPTVVAVNGLALGGGLE 125

Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180
           + LAAD R++S +A++GLPEV LGI+PGFGGTVRLPRLIG + A++WI SG   KA+DAL
Sbjct: 126 LALAADVRMLSDSARIGLPEVGLGIFPGFGGTVRLPRLIGVEAALQWIMSGTPRKADDAL 185

Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240
           + GAVDAVV P +L+ AAL+     VA   D   RR+  L  + + A E +     A   
Sbjct: 186 RAGAVDAVVPPPELREAALERLHGLVASP-DWSERRKEALSPV-VRAGEDLAPIFAAAKA 243

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300
            A + GP+ PA +  ++ I+ AA   RD AL +EA  F  +A+T  A++L+ +F+NDQ +
Sbjct: 244 KARKTGPHLPASLAVVELIESAAGVDRDAALALEARAFAHIARTPAARALVAVFINDQAV 303

Query: 301 KKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKL 360
           KK  K+    A+ V  AAVLGAGIMGGGIAYQSA+ G P++MKDI +  + +G+ +A  L
Sbjct: 304 KKTTKQQTRAARPVSRAAVLGAGIMGGGIAYQSAVCGIPVIMKDIAQSALDLGMTQAGAL 363

Query: 361 LGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVK 420
           L KRVE G L+ AK    L  IRP ++Y      D++VEAVVEN  +K+AVLAE+E  ++
Sbjct: 364 LAKRVETGALSSAKADGILASIRPGLTYDGIAEADVIVEAVVENIAIKRAVLAELEEHIR 423

Query: 421 EDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVA 480
            DA++A+NTS++ ++ LA+ L+ PENF GMHFFNPVH MPLVEVI+G  T   A+AT V 
Sbjct: 424 PDAVVATNTSSLLVADLARDLEWPENFVGMHFFNPVHRMPLVEVIQGPHTSPEAVATIVG 483

Query: 481 YAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYL 540
           YA  MGK+P+VV DCPGFLVNR+L     GF +L+  G DF+RID  ME FGWPMGPA+L
Sbjct: 484 YASAMGKTPVVVRDCPGFLVNRILAANVLGFLRLIHDGADFLRIDAAMEGFGWPMGPAWL 543

Query: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKP 600
            DV+G+DT  H  +V+A G+P+RM VE  TA+DVM E+ R GQK+G GFY YE D  G  
Sbjct: 544 QDVIGMDTSRHVIEVIAAGYPERMRVEFATALDVMVESKRFGQKSGAGFYRYEADAAGHQ 603

Query: 601 KKVTDPQAYEVLKPIVV-EQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLI 659
           +KV DP    +L  +     R ++DE+IV   M+P+ LET RCLEDG+V +AAEADM LI
Sbjct: 604 RKVVDPDVGALLATVQPGGSRIISDEEIVQRTMLPMILETARCLEDGVVGSAAEADMALI 663

Query: 660 YGIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNG 710
            GIGFP   GGAL Y D +G    +   D+YA LG LYHPT ++R +A +G
Sbjct: 664 LGIGFPRHLGGALHYADELGAKTIMEWCDRYANLGPLYHPTPRMRRLAVDG 714


Lambda     K      H
   0.318    0.137    0.388 

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: 1189
Number of extensions: 51
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: 715
Length of database: 727
Length adjustment: 40
Effective length of query: 675
Effective length of database: 687
Effective search space:   463725
Effective search space used:   463725
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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