Alignments for a candidate for aspS2 in Rhizorhabdus wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Rhizorhabdus wittichii RW1

Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_029991820.1 SWIT_RS00210 aspartate--tRNA ligase

Query= reanno::Caulo:CCNA_01969
         (612 letters)



>NCBI__GCF_000016765.1:WP_029991820.1
          Length = 592

 Score =  789 bits (2038), Expect = 0.0
 Identities = 402/612 (65%), Positives = 464/612 (75%), Gaps = 25/612 (4%)

Query: 4   MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63
           MHAYRTHNCG LRA D G+ VRLSGW+HRKRDHG L+F+DLRDHYGLTQ+V   E+  F 
Sbjct: 1   MHAYRTHNCGQLRAQDVGSQVRLSGWVHRKRDHGNLLFVDLRDHYGLTQIVTDIESEAFR 60

Query: 64  VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123
            +ERLR ESV+ + G+V+AR    VNPNL TGEIEIR   V V S A ELPLPV GE DY
Sbjct: 61  QLERLRVESVVTITGDVVARAGEAVNPNLATGEIEIRAREVSVQSTAQELPLPVAGEADY 120

Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183
           PE+IRL++R+LDLRR+ +H NIVLRS VI SIR RM  QGF E+QTPILTASSPEGARDF
Sbjct: 121 PEDIRLRYRFLDLRRDRIHANIVLRSNVIASIRRRMIDQGFTEYQTPILTASSPEGARDF 180

Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242
           LVPSR+HP KFYALPQAPQ FKQLLMV+GFDRYFQIAPCFRDED RADRS  EFYQLD E
Sbjct: 181 LVPSRIHPGKFYALPQAPQMFKQLLMVAGFDRYFQIAPCFRDEDARADRSPGEFYQLDFE 240

Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302
           MSFVTQEDVFAAIEPV+HGVFEEF+NG+ V+P                   F R+ Y  +
Sbjct: 241 MSFVTQEDVFAAIEPVLHGVFEEFANGRAVTP-----------------APFPRIAYRDA 283

Query: 303 MAWYGSDKPDLRNPIKMANVSEHFRDGGFGLFAKILGADAKNQVWAIPAPTGG--SRAFC 360
           M  YGSDKPDLRNP+++ +V+EHF+  GFGLFA+I+  +    V AIPAP  G  SR F 
Sbjct: 284 MLRYGSDKPDLRNPLEITDVTEHFQGSGFGLFARIV--EGGGVVRAIPAPGAGAKSRKFF 341

Query: 361 DRMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLG-EPTQALMESLGLGAGDAAFFVAG 419
           D MN WA+ +G  GLGY+  +   G  GGPIAKN G E T  L+ +LGLG  D  FF AG
Sbjct: 342 DDMNDWARAQGHAGLGYI--NIKGGEAGGPIAKNHGEEATAKLIAALGLGPDDGVFFAAG 399

Query: 420 DPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFSMPQG 479
                AK AG ARTRVG EL L+++  FKFCW+VDFPMFE++E+ KK+DFSHNPFSMPQG
Sbjct: 400 KELATAKLAGAARTRVGEELGLIEQGVFKFCWVVDFPMFEYDEDAKKIDFSHNPFSMPQG 459

Query: 480 GLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEEQFGG 539
            +EALET DPL I AYQYDIVCNG EL SGAIRNH+PEIM KAF  AGY  E VEE F G
Sbjct: 460 EMEALETMDPLDILAYQYDIVCNGVELSSGAIRNHRPEIMYKAFEIAGYSQEQVEENFSG 519

Query: 540 MLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVLDKQL 599
           MLNAF++GAPPHGG APGIDRIVMLLAD+  IREV+ FP+NQ+ +DL+M AP+ V  KQL
Sbjct: 520 MLNAFKFGAPPHGGSAPGIDRIVMLLADEPNIREVVLFPMNQKAEDLMMGAPSQVSLKQL 579

Query: 600 KELHIRTAPPIK 611
           +EL+IR     K
Sbjct: 580 RELNIRVVEQSK 591


Lambda     K      H
   0.321    0.139    0.425 

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: 1123
Number of extensions: 49
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: 612
Length of database: 592
Length adjustment: 37
Effective length of query: 575
Effective length of database: 555
Effective search space:   319125
Effective search space used:   319125
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: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis